Organizing cell renewal in the intestine: stem cells, signals and combinatorial control

The lining of the intestine is renewed at an extraordinary rate, outpacing all other tissues in the vertebrate body. The renewal process is neatly organized in space, so that the whole production line, from the ever-youthful stem cells to their dying, terminally differentiated progeny, is laid out to view in histological sections. A flurry of recent papers has clarified the key regulatory signals and brought us to the point where we can begin to give a coherent account, for at least one tissue, of how these signals collaborate to organize the architecture and behaviour of a stem-cell system.     

The comparative biology of pulmonary surfactant: past, present and future

Richard E. Pattle contributed enormously to the biology of the pulmonary surfactant system. However, Pattle can also be regarded as the founding father of comparative and evolutionary research of the surfactant system. He contributed eight seminal papers of the 167 publications we have located on this topic. In particular, Pattle produced a synthesis interpreting the evolution of the surfactant system that formed the foundation for the area. Prepared 25 years ago this synthesis spawned the three great discoveries in the comparative biology of the surfactant system: (1) that the surfactant system has been highly conserved throughout the enormous radiation of the air breathing vertebrates; (2) that temperature is the major selective condition that influences surfactant composition; (3) that acting as an anti-adhesive is one primitive and ubiquitous function of vertebrate surfactant. Here we review the literature and history of the comparative and evolutionary biology of the surfactant system and highlight the areas of comparative physiology that will contribute to our understanding of the surfactant system in the future. In our view the surfactant system is a neatly packaged system, located in a single cell and highly conserved, yet spectacularly complex. The surfactant system is one of the best systems we know to examine evolutionary processes in physiology as well as gain important insights into gas transfer by complex organisms.     

RFLP approach to breeding for quantitative traits in plants—a critique

A number of recent papers suggest that use of RFLPs as markers offers a clear advantage in breeding for improvement in quantitative traits (QTs). The concepts underlying establishment of linkage between RFLP markers and QT loci stem from three papers on tomato published during 1987–1991. Essentially, continuously varying QT phenotypes are assigned to RFLP genotype classes, which can be considered to be determined by a single, diallelic gene with codominant alleles. Linkage is inferred through statistical analysis. Similarly, interaction between markers and QT is also tested by an analysis of variance. Here, the statistical methods employed in these three papers to detect linkage are critically evaluated, especially because subsequent investigations take the concepts developed in these papers as proven. In this paper, we examine the three fundamental papersde novo. We scrutinize the methods employed and the inferences drawn to bring to light what we believe are conceptual drawbacks.     

Learning biology through research papers: a stimulus for question-asking by high-school students

Question-asking is a basic skill, required for the development of scientific thinking. However, the way in which science lessons are conducted does not usually stimulate question-asking by students. To make students more familiar with the scientific inquiry process, we developed a curriculum in developmental biology based on research papers suitable for high-school students. Since a scientific paper poses a research question, demonstrates the events that led to the answer, and poses new questions, we attempted to examine the effect of studying through research papers on students' ability to pose questions. Students were asked before, during, and after instruction what they found interesting to know about embryonic development. In addition, we monitored students' questions, which were asked orally during the lessons. Questions were scored according to three categories: properties, comparisons, and causal relationships. We found that before learning through research papers, students tend to ask only questions of the properties category. In contrast, students tend to pose questions that reveal a higher level of thinking and uniqueness during or following instruction with research papers. This change was not observed during or following instruction with a textbook. We suggest that learning through research papers may be one way to provide a stimulus for question-asking by high-school students and results in higher thinking levels and uniqueness.     

A list of personal perspectives with selected quotations,along with lists of tributes,historical notes,Nobel and Kettering awards related to photosynthesis

The history of photosynthesis research can be found in original papers and books. However, a special history is available from the prefatory chapters and the personal perspectives of various researchers who published them in several journals over the last 40 years. We have compiled a list of such perspectives published since 1964. Selection is not easy, especially of authors who were not directly engaged in photosynthesis research; some are included for their special insights related to central issues in the study of photosynthesis. Our journal, Photosynthesis Research, contains other valuable historic data in the occasional tributes, obituaries and historical notes, that have been published. Lists of these items are included. This article ends by listing the Nobel prizes related to photosynthesis and the Kettering Awards for Excellence in Photosynthesis Research. Wherever possible, a web page address is provided. The web page addresses have been taken from the article `Photosynthesis and the Web: 2001' by Larry Orr and Govindjee, available at http://www.life.uiuc.edu/govindjee/photoweb and at http://photoscience.la.asu.edu/photosyn/ photoweb/default.html. ‘When I find a bit of leisure I trifle with my papers. This is one of the lesser frailities. – Horace, Satires I, IV. This revised version was published online in June 2006 with corrections to the Cover Date.     

Construction and nanomechanical properties of the exoskeleton of the barnacle, Amphibalanus reticulatus

Barnacles are some of the major inhabitants of intertidal zones and have calcite-based exoskeleton to anchor and armor their tissues. Structural characterization studies of the specie Ambhibalanus reticulatus were performed to understand the construction of the exoskeleton which forms a light-weight yet stiff structure. The parietal shell is constructed of six compartments to yield a truncated cone geometry, which is neatly fixed onto the basal shell that attaches the organism to the substrate surface. The connections among the different compartments happen through sutured edges and also have chemical interlocking to make the junctions impermeable. Also, the shell parts are furnished with hollow channels reducing the overall mass of the construction. The structure and functions of different parts of the exoskeleton are identified and outlined. Finally, the mechanical properties such as modulus, hardness and fracture toughness of the exoskeleton obtained by indentation techniques are discussed.     

Outside of the box: recent news about phospholipid translocation by P4 ATPases

The P4 subfamily of P-type ATPases includes phospholipid transporters. Moving such bulky amphipathic substrate molecules across the membrane poses unique mechanistic problems. Recently, three papers from three different laboratories have offered insights into some of these problems. One effect of these experiments will be to ignite a healthy debate about the path through the enzyme taken by the substrate. A second effect is to suggest a counterintuitive model for the critical substrate-binding site. By putting concrete hypotheses into play, these papers finally provide a foundation for investigations of mechanism for these proteins.     

Back Cover Image,Volume 117, Number 2, February 2020

During the manufacturing process, solutions of protein-based drugs are exposed to hydrodynamic forces, which can potentially affect protein stability and aggregation. Despite being an area of extensive investigation, the effect of hydrodynamic flow on protein aggregation is still controversial. In this study, we designed an experimental setup that allowed us to investigate flow- and interface-induced protein aggregation of two model immunoglobulins in the presence of well-defined flow stresses and solid–liquid interfaces. Within the range of shear rates typically encountered in bioprocessing (), we observed that increasing the shear rate by three orders of magnitude had a negligible effect on protein aggregation. By contrast, changes in the materials of the syringe barrels had a dramatic effect on the monomer loss, demonstrating the key role of solid–liquid interfaces in flow-induced aggregation. This finding was confirmed by the observed inverse dependence of the aggregation rate on the initial protein concentration, which is inconsistent with mechanisms of protein aggregation in bulk solution. Overall, our results reveal the presence of a synergistic effect of interfaces and hydrodynamic flow in flow-induced protein aggregation, which arises from the formation of protein particles or films on interfaces followed by displacement by flow or mechanical scraping.     

Protocols, Toolboxes and Resource papers

In the August 2009 issue of Autophagy, I indicated that we were launching a new category of article, Protocols. At that time, I noted that we would ultimately be placing these articles on a new site online. Well, that time has finally arrived (see www.landesbioscience.com/journals/autophagy/protocols/ for links to these papers). Therefore, it seems appropriate for me to briefly distinguish among three types of community-oriented papers, Protocol, Toolbox and Resource.     

Functional significance of periostin in excisional skin repair: Is the devil in the detail?

In the past year, three papers have been published exploring the role of the matricellular protein periostin in excisional skin repair. These papers all show a delay in wound closure and the kinetics of this delay are strikingly similar across the three reports. The similarities between these papers end, however, when each investigates the mechanism through which periostin influences skin repair. Three proposed mechanisms have been identified: (1) myofibroblast differentiation, (2) keratinocyte proliferation and (3) fibroblast proliferation and migration. The aim of this commentary is to compare and contrast the three studies performed to date in an attempt to decipher the role of periostin in the repair of full-thickness skin wounds.     

The Hall of Mirrors: Orientalism, Anthropology, and the Other

Anthropologists specialize in human difference and thus cannot escape the dialectics of sameness and difference. Yet studying Others has been the object of attack in recent years, most notably by Edward Said, who sees the mere postulation of difference as dangerous, as a dehumanizing activity that valorizes Self and vilifies Other. In fact the situation is not so simple: the Other may be a model to be emulated or a mirror of the shadow side of the Self. Selfhood and Otherness, virtue and vice, are subject to ceaseless negotiation and reinterpretation. In this hall of mirrors, the Self and the Other cannot be neatly distinguished.     

Functional significance of periostin in excisional skin repair

In the past year, three papers have been published exploring the role of the matricellular protein periostin in excisional skin repair. These papers all show a delay in wound closure and the kinetics of this delay are strikingly similar across the three reports. The similarities between these papers end, however, when each investigates the mechanism through which periostin influences skin repair. Three proposed mechanisms have been identified: (1) myofibroblast differentiation, (2) keratinocyte proliferation and (3) fibroblast proliferation and migration. The aim of this commentary is to compare and contrast the three studies performed to date in an attempt to decipher the role of periostin in the repair of full-thickness skin wounds.     

Protein translation, 2007

Translation of RNA to protein is essential for life. It should perhaps not be surprising, therefore, that appropriate regulation of translation plays a key role in determining longevity. This Hot Topic article discusses papers published in the last year related to the importance of translation and its regulation by signaling through the target of rapamycin kinase, in modulating aging and age-associated diseases.     

Pyridine to aniline: An exceptional biologically driven rearrangement

During the course of our study on the innovative ligand for nicotinic acetylcholinergic receptors, LNAChR, and in order to assess activity and toxicity profiles of the drug’s metabolites, synthesis of the main metabolites was undertaken. This synthesis work was done in parallel by organic chemistry and by biotransformation of LNAChR. Filamentous fungus Aspergillus alliaceus (NRRL 315) neatly afforded three of the main metabolites, one of which arose from a very unexpected and very uncommon rearrangement.     

Herpetological research in zoos: A literature survey, 1977–1981

Herpetological zoo research published in three journals between 1977 and 1981 was surveyed. Fifty-three of 1,084 published papers involved zoos. Research for 30 papers was conducted in zoos. Just under three fourths of zoo papers involved behavioral research. Sixteen zoos were involved in research in this survey.     

Order-disorder phenomena in myelinated nerve sheaths. IV. The disordering effects of high levels of local anaesthetics on rat sciatic and optic nerves.

Sequences of 15 minute X-ray scattering spectra were recorded with rat sciatic and optic nerves, superfused with tetracaine-containing Ringer solutions. The spectra were analysed using the algorithm advocated in this series of papers. The main results, as a function of the time of exposure to tetracaine, were: the mean value of the repeat distance increases; its variance decreases; the average number of membrane pairs per coherent domain decreases; the fraction of isolated membrane pairs increases. Eventually, the spectra were observed to give way to the continuous intensity curve of a single, isolated membrane pair. At all stages of the experiment the continuous intensity curves were found to differ from one type of nerve to the other, and to be invariant, for each type of nerve, with respect to the tetracaine treatment. The X-ray scattering study clearly identified the nature of the structural differences between the two types of myelin sheaths: in that of native sciatic nerves, packing disorder preferentially affects the cytoplasmic space of the membrane pair, and tetracaine disrupts the packing in that space; in the myelin of optic nerves it is the external space that is preferentially affected by packing disorder and disrupted by tetracaine. The time-course of the structure parameters showed that, at any stage of the experiment, tetracaine acts preferentially on the more highly disordered regions of the structure and totally disrupts them. These results corroborate earlier conclusions reported in the previous papers of this series. An electron microscope study was also performed on tetracaine-treated nerves: the results, in close agreement with those of the X-ray scattering study, neatly confirm the conclusions given above. In a more general way, the remarkable agreement between the results of the analysis of the X-ray scattering spectra and the electron microscope observations strongly supports the validity of the physical model used in this series of papers and the correctness of the mathematical treatment that we advocate. Finally, the relations between this work and the work of others are discussed. It must be stressed that the present work bears on the toxic rather than on the anaesthetic effects of tetracaine.     

Reasons for failure of genetic classifications of South Amerind populations

Previous attempts to classify South American Indian tribes according to genetic characteristics have failed to yield a hierarchical system of relationships. This can be explained by the facts that (1) tribal populations did not evolve through sequential fissions but through frequent fusions of groups with diverse histories and (2) allele frequencies have been held at nearly common values by intertribal migration or balancing selection. A valid model must allow for fusion and mixed populations as well as for fission; factor analysis or newer methods of fuzzy mathematics permit this. The effects of migration and balancing can be made more manageable by partitioning them according to the limited time periods recorded by haplotypes. An initial attempt using factor analysis and HLA haplotype data on 19 rain forest tribes revealed two overlapping clusters that are largely but not neatly separated by the lower Amazon River. Several tribes, especially in the west, were excluded from these clusters.     

Screening and evaluation of resistance to downy mildew (Peronospora parasitica) and clubroot (Plasmodiophora brassicae) in genetic resources of Brassica oleracea

52 entries including landraces, old cultivars and wild accessions of B. oleracea and closely related Brassica species were screened for resistance against downy mildew and clubroot. Several accessions resistant to downy mildew and a few to clubroot were found. Genetic inheritance of the resistance in downy mildew was investigated by screening F1 and BC1F1 offspring from three resistant landrace accessions crossed with both a resistant and a susceptible father. The seedling resistance against downy mildew was found to be inherited recessively. This is a bit surprising as earlier papers mostly report of inheritance controlled by a single dominant gene. Previous screenings of B. oleracea resistance against downy mildew at the cotyledon stage have been done with P. parasitica isolated from B. oleracea as the original host plant. The recessive nature of the cotyledon resistance found in this screening might be due to the fact that the P. parasitica isolate was collected from B. napus fields. The clubroot seedling resistance was found to be controlled by recessive inheritance after screening the F1 offspring, this in agreement with earlier results/reports.     

Death by design: apoptosis, necrosis and autophagy

Apoptosis is the principal mechanism by which cells are physiologically eliminated in metazoan organisms. During apoptotic death, cells are neatly carved up by caspases and packaged into apoptotic bodies as a mechanism to avoid immune activation. Recently, necrosis, once thought of as simply a passive, unorganized way to die, has emerged as an alternate form of programmed cell death whose activation might have important biological consequences, including the induction of an inflammatory response. Autophagy has also been suggested as a possible mechanism for non-apoptotic death despite evidence from many species that autophagy represents a survival strategy in times of stress. Recent advances have helped to define the function of and mechanism for programmed necrosis and the role of autophagy in cell survival and suicide.