CHROMOSIN,A DESOXYRIBOSE NUCLEOPROTEIN COMPLEX OF THE CELL NUCLEUS

A desoxyribose nucleoprotein complex, which we have referred to as a chromosin, has been prepared from a great variety of cells, mainly animal but also plant and bacterial. A chromosin is derived from the cell nucleus. In the course of preparation precautions have been taken to prevent contamination by cytoplasmic constituents. To assure the nuclear origin of all components of chromosin, nuclei have in several instances been isolated before extraction was begun. Because of the precautions taken, chromosins do not contain detectable quantities of ribose nucleoproteins; but, incidentally, extraction of ribose nucleoproteins, free of desoxyribose compounds, has also been described in this paper. A typical chromosin contains 3 components: desoxyribose nucleic acid, histone, and non-histone protein. The nucleic acid, being highly polymerized, is exceedingly viscous when dissolved and fibrous when precipitated. Histone and non-histone protein differ from each other in a number of ways, of which one of the most definite is that whereas a histone contains no more than traces of tryptophane, the non-histone protein of chromosin contains nearly 1 per cent of tryptophane. In neutral physiological saline both proteins can combine with nucleic acid. With the isolation of chromosins from so many different kinds of cells, it can now be seen that (contrary to the view expressed by Kossel) histones are present in most animal cells and at least in some plant and bacterial cells. Chromosin prepared from the Type III pneumococcus is active in transforming the type of a pneumococcus culture. It has been pointed out that it is not yet known whether or not protein is a necessary constituent of the transforming agent. To extract chromosin from a cell M NaCl is used. When dissolved in M NaCl the nucleic acid and histone components of a chromosin are to a considerable extent dissociated. They are not dissociated when the chromosin is dissolved in 0.02 M NaCl, but in this medium a partial depolymerization of the nucleic acid occurs. A chromosin should certainly not be considered to be a definite chemical compound. It is a complex extracted from chromatin, which is itself a complicated nuclear structure. And in the course of extraction, it need hardly be said, the structure of chromatin has been considerably changed. To avoid complications it has been considered an advantage in this work to begin with isolated nuclei, and it would clearly be a further simplification to begin chemical procedures only after the chromosomes themselves have been isolated. This is now being accomplished, and it is found that the methods described in this paper are of value in learning how the substances present in a chromosin are put together in a chromosome.     

THE NUCLEOPROTAMINE OF TROUT SPERM

The nucleoprotamine of trout sperm can be extracted completely with 1 M sodium chloride. On reducing the salt concentration to 0.14 M, physiological saline, the nucleoprotamine precipitates in long, fibrous strands. When the nucleoprotamine, dissolved in M NaCl, is dialyzed all the protamine diffuses through the membrane leaving behind highly polymerized, protein-free desoxyribose nucleic acid. The nucleoprotamine constitutes 91 per cent of the lipid-free mass of the sperm nucleus. While nucleoprotamine is being extracted by M NaCl a stage is reached at which the sperm chromosomes are clearly visible.     

The Jurassic GenusReinholdella Brotzen (1948) (Foram.)

In this treatise the author describes two species from the Lias, and four from the Dogger. One liassic species is already known (Reinholdella macfadyeni [Ten Dam]) from the Upper Lias (Bifrons-Zone), England, the other one was found by Dr.Bartenstein in Luxemburg, Lias δ Grenze ε, and has been namedReinholdella pachyderma nov. spec. The species from the Dogger areReinholdella dreheri (Bartenstein) and three new species, viz.Reinholdella brandi nov. spec.,Reinholdella ornata nov. spec. andReinholdella epistominoides nov. spec. The genusReinholdella has obviously derived from the genusConorboides Hofker (1951) and the speciesR. epistominoides proves that the genusEpistomina is related withReinholdella. It may be thatReinholdella is related withAsterigerina; but the large gap in the Cretaceous, where noReinholdella is found nor any species ofAsterigerina, contradicts this view.     

Chemistry and clinical uses of the protein components involved in blood clotting

Recent advances in the chemistry of the clotting process include:

1. 1)
   The preparation of highly purified prothrombin and thrombin from beef blood by Seegers and his associates.     
   
   

THE CHEMICAL COMPOSITION OF ISOLATED CHROMOSOMES

By means of 1 M NaCl isolated lymphocyte chromosomes can be separated into two fractions, each of which contains nucleoprotein. The fraction soluble in M NaCl consists largely of desoxyribose nucleohistone, and constitutes 90 to 92 per cent of the mass of the chromosome. The insoluble residue (the residual chromosome is a coiled thread containing some 12 to 14 per cent of ribose nucleic and about one-fifth as much desoxyribose nucleic acid; the residual chromosome accounts for 8 to 10 per cent of the mass of the chromosome. The staining of chromosomes—whether by the Feulgen procedure, by hematoxylin, orcein, or by basic dyes such as crystal violet—is due to the nucleohistone fraction which contains about 96 per cent of the nucleic acid of the chromosome. The form of the chromosome is due primarily to the protein thread of the residual chromosome. This thread is the only linear structure of microscopic dimensions in the chromosome that is not readily dispersed. When chromosomes are broken, it must be supposed that a break is made in the protein thread of the residual chromosome. The foregoing provides evidence for considering the residual chromosome to be the basis of the linear order of the genes. This would mean either that the residual chromosome is a structure around which the genes are organized or that the genes form part of its substance.     

Kinetics of heterochiral strand displacement from PNA–DNA heteroduplexes

Dynamic DNA nanodevices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation remains challenging due to nuclease degradation and other cellular factors. Use of l-DNA, the nuclease resistant enantiomer of native d-DNA, provides a promising solution. On this basis, we recently developed a strand displacement methodology, referred to as ‘heterochiral’ strand displacement, that enables robust l-DNA nanodevices to be sequence-specifically interfaced with endogenous d-nucleic acids. However, the underlying reaction – strand displacement from PNA–DNA heteroduplexes – remains poorly characterized, limiting design capabilities. Herein, we characterize the kinetics of strand displacement from PNA–DNA heteroduplexes and show that reaction rates can be predictably tuned based on several common design parameters, including toehold length and mismatches. Moreover, we investigate the impact of nucleic acid stereochemistry on reaction kinetics and thermodynamics, revealing important insights into the biophysical mechanisms of heterochiral strand displacement. Importantly, we show that strand displacement from PNA–DNA heteroduplexes is compatible with RNA inputs, the most common nucleic acid target for intracellular applications. Overall, this work greatly improves the understanding of heterochiral strand displacement reactions and will be useful in the rational design and optimization of l-DNA nanodevices that operate at the interface with biology.     

Ueber das an Lebewesen im allgemeinsten beobachtbare biophysikalische Gesetz,zugleich eine Zusammenfassung meiner,sich auf die den Entwicklungsgang der Lebewesen lenkenden biophysikalischen Faktoren bestehenden bisherigen Forschungen

Author cultivated fermenting cells (Scccharomyces spec.) in must of grapes and measured the various vital phenomena. The data thus received described in a rectangular co-ordinate as a function of time, found three kinds of characteristic curves in every vital phenomenon (whether belonging to the group of feeding, growth or that of increase): I. the curve described bySachs in 1873 and called the curve of the great period of evolution (Fig. 1:s). 2. the one described byM. G. Harting in 1845, and the curve of individual or ontogenetic evolution (Fig. 1:S). 3. the undulatory curve similar to a sinus-cosinus function, deduced in theory by author and later on, in 1915, also found on an experimental basis (Fig. 3). — Analysing these curves, author demonstrates that they are in the closest relationship with each other. The course ofSachs' great period is identical with the function of the aperiodically mitigated vibromotion; the course ofHarting's ontogenetic curve is identical with the integral of the previous aperiodic function; the undulatory curve discovered by the author, and the one belonging to the philogenesis of evolution, consist of two details, one of the members is formed from the function of aperiodically mitigated vibromotion, and the other from a function of periodically mitigated vibration. — Mitigated vibromotion, according to our present knowledge can only arise if a body capable of vibration is simultaneously affected by a force establishing movement and a resistance mitigating the movement. In the living organism, on this basis, there is also a force and a resistance. The living organism obtains this force from food while the resistance is rooted in the construction of the cell. The author proves that the cells which no longer divide (the so-called permanent tissueforming cells) follow an aperiodical vibromotor course in their development while in the development of the continually dividing, so-called meristematic cells, owing to the periodic change of division and regeneration, the potential of the energy accommodates itself to the periodic vibromotor course. Both forms of development are derived from the identical differential equation: d²s/dt²=?w²s?2r ds/dt, the only difference between the two phenomena is that by aperiodic oscillation it is r²>w² while by periodic it is r²2 and this brings about the difference in the development of the cells. Thus the laws of ?biomotoric energy” following vibromotion constitute the most general law in living organism. The organism lives as long as the biomotoric energy is active, if the action of this energy ceases, death ensues. The most essential result of this research work is that we have become acquainted in regard to both cases with the w, r, v₀ factors regulating the qualities of two chief types of living cells, the meristematic and those incapable of division as in these equations, the constants changing according to the biological conditions, and that we can accurately follow the course of the phenomena with the method of theoretic physics and furthermore, that we have found the connection between these two chapters of evolution.     

BAZ2A safeguards genome architecture of ground‐state pluripotent stem cells

Chromosomes have an intrinsic tendency to segregate into compartments, forming long‐distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground‐state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin sub‐domains within the active A compartment, which intersect through long‐range contacts. We found that ground‐state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A‐dependent manner. Finally, ground‐state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.     

Interaction of poly-L-lysine with chromatin. Inhibition of in situ priming for Escherichia coli DNA polymerase

The priming capacity of chromatin of fixed nuclei and chromosomes for exogenous DNA polymerase can be evaluated radioautographically by the incorporation of labeled nucleotides. It had previously been reported that acid fixation or acid treatment of alcohol-fixed tissues led to increased priming when calf thymus DNA polymerases, specific for single-stranded DNA, were used. We employed Escherichia coli DNA polymerase and sequential treatments of the fixed tissue with acid and poly-L-lysine in order to elucidate the mechanism through which the acid effect is produced. Acid treatment enhanced chromatin priming for the E coli DNA polymerase, and saturation of the chromatin with poly-L-lysine strongly inhibited the reaction. This inhibition was reversible through subsequent treatment with acid. Wide differences in priming were observed between cell types of alcohol-fixed chicken blood smears: thrombocyte and lymphocyte nuclei exhibited strong priming ability whereas erythrocyte nuclei failed to support any detectable priming. We conclude that the acid effect is readily interpretable in terms of acid-mediated changes in the association between DNA and protein in the chromatin complex.     

Human shelterin protein POT1 prevents severe telomere instability induced by homology‐directed DNA repair

The evolutionarily conserved POT1 protein binds single‐stranded G‐rich telomeric DNA and has been implicated in contributing to telomeric DNA maintenance and the suppression of DNA damage checkpoint signaling. Here, we explore human POT1 function through genetics and proteomics, discovering that a complete absence of POT1 leads to severe telomere maintenance defects that had not been anticipated from previous depletion studies in human cells. Conditional deletion of POT1 in HEK293E cells gives rise to rapid telomere elongation and length heterogeneity, branched telomeric DNA structures, telomeric R‐loops, and telomere fragility. We determine the telomeric proteome upon POT1‐loss, implementing an improved telomeric chromatin isolation protocol. We identify a large set of proteins involved in nucleic acid metabolism that engage with telomeres upon POT1‐loss. Inactivation of the homology‐directed repair machinery suppresses POT1‐loss‐mediated telomeric DNA defects. Our results unravel as major function of human POT1 the suppression of telomere instability induced by homology‐directed repair.     

DNA-protein binding in interphase chromosomes

The metachromatic dye, azure B, was analyzed by microspectrophotometry when bound to DNA fibers and DNA in nuclei with condensed and dispersed chromatin. The interaction of DNA and protein was inferred from the amount of metachromasy (increased β/α-peak) of azure B that resulted after specific removal of various protein fractions. Dye bound to DNA-histone fibers and frog liver nuclei fixed by freeze-methanol substitution shows orthochromatic, blue-green staining under specific staining conditions, while metachromasy (blue or purple color) results from staining DNA fibers without histone or tissue nuclei after protein removal. The dispersed chromatin of hepatocytes was compared to the condensed chromatin of erythrocytes to see whether there were differences in DNA-protein binding in "active" and "inactive" nuclei. Extraction of histones with 0.02 N HCl, acidified alcohol, perchloric acid, and trypsin digestion all resulted in increased dye binding. The amount of metachromasy varied, however; removal of "lysine-rich" histone (extractable with 0.02 N HCl) caused a blue color, and a purplish-red color (µ-peak absorption) resulted from prolonged trypsin digestion. In all cases, the condensed and the dispersed chromatin behaved in the same way, indicating the similarity of protein bound to DNA in condensed and dispersed chromatin. The results appear to indicate that "lysine-rich" histone is bound to adjacent anionic sites of a DNA molecule and that nonhistone protein is located between adjacent DNA molecules in both condensed and dispersed chromatin.     

Insect trace fossils in glyptodonts from Uruguay

Abstract

The association of vertebrate remains and invertebrate traces, although less studied than other bioerosion traces, provides important paleoecological information. This report describes Cubiculum ornatum Roberts, Rogers, and Foreman 2007 Roberts, E., R. Rogers, and B. Foreman. 2007. Continental insect borings in dinosaur bone: examples from the Late Cretaceous of Madagascar and Utah. Journal of Paleontology 81(1):201–208.[Crossref], [Web of Science ®] , [Google Scholar], Osteocallis Roberts, Rogers, and Foreman 2007 Roberts, E., R. Rogers, and B. Foreman. 2007. Continental insect borings in dinosaur bone: examples from the Late Cretaceous of Madagascar and Utah. Journal of Paleontology 81(1):201–208.[Crossref], [Web of Science ®] , [Google Scholar] and other unidentified insect traces from the dermal skeletal remains of glyptodonts found in Uruguay. They come from the Fray Bentos Formation (Late Oligocene), the Camacho Formation (Late Miocene) and the Dolores Formation (Late Pleistocene-Early Holocene). The reported traces were likely made by sarcosaprophagous beetles, which indicate depositional conditions with dry episodes in a warm climate for the referred stratigraphical units.     

Ichnogeny and bivalve bioerosion: examples from shell and wood substrates

Abstract

The ichnospecies Gastrochaneolites dijugus Kelly and Bromley 1984 Kelly, S. R. A., and R. G. Bromley. 1984. “Ichnological Nomenclature of Clavate Borings.” Palaeontology 27: 793–807.[Web of Science ®] , [Google Scholar] and Teredolites longissimus Kelly and Bromley 1984 Kelly, S. R. A., and R. G. Bromley. 1984. “Ichnological Nomenclature of Clavate Borings.” Palaeontology 27: 793–807.[Web of Science ®] , [Google Scholar], attributed to the boring activity of gastrochaenoid and pholadid bivalves, are described respectively from the Miocene Vilanova Basin and the Pliocene Almería-Níjar Basin. Miocene and Pliocene traces are preserved as positive casts associated to invertebrate shells and wood fragments, respectively; in both cases, the host substrate (shells and wood) has been lost almost entirely by different taphonomic processes (mainly dissolution). For the first time in the fossil record, the complete ichnogenetic sequence of these two ichnospecies is described and figured.     

Versatile CRISPR/Cas9-mediated mosaic analysis by gRNA-induced crossing-over for unmodified genomes

Mosaic animals have provided the platform for many fundamental discoveries in developmental biology, cell biology, and other fields. Techniques to produce mosaic animals by mitotic recombination have been extensively developed in Drosophila melanogaster but are less common for other laboratory organisms. Here, we report mosaic analysis by gRNA-induced crossing-over (MAGIC), a new technique for generating mosaic animals based on DNA double-strand breaks produced by CRISPR/Cas9. MAGIC efficiently produces mosaic clones in both somatic tissues and the germline of Drosophila. Further, by developing a MAGIC toolkit for 1 chromosome arm, we demonstrate the method’s application in characterizing gene function in neural development and in generating fluorescently marked clones in wild-derived Drosophila strains. Eliminating the need to introduce recombinase-recognition sites into the genome, this simple and versatile system simplifies mosaic analysis in Drosophila and can in principle be applied in any organism that is compatible with CRISPR/Cas9.

Analysis of mosaic animals has been crucial in developmental and cell biology; this study describes a versatile, simple, and likely widely-applicable technique, MAGIC (mosaic analysis by gRNA-induced crossing-over), for generating mosaic animals based on DNA double-strand breaks produced by CRISPR/Cas9.     

Macroborings in Otodus megalodon and Otodus chubutensis shark teeth from the submerged shelf of Onslow Bay,North Carolina,USA: implications for processes of lag deposit formation

Abstract

The shallow continental shelf in the Cape Fear Region of southwestern Onslow Bay, North Carolina, contains lag deposits with an abundance of megatoothed shark teeth belonging to Otodus megalodon (Agassiz 1835) and Otodus chubutensis (Ameghino 1906) that derive from the Pliocene Yorktown and Miocene Pungo River formations, respectively. These teeth exhibit different frequencies and orientations of macroborings identified as Gastrochaenolites torpedo Kelly and Bromley (1984 Kelly, S., and R. Bromley. 1984. “Ichnological Nomenclature of Clavate Borings.” Palaeontology 27: 793–807.[Web of Science ®] , [Google Scholar]), Gastrochaenolites lapidicus Kelly and Bromley (1984 Kelly, S., and R. Bromley. 1984. “Ichnological Nomenclature of Clavate Borings.” Palaeontology 27: 793–807.[Web of Science ®] , [Google Scholar]), Maeandropolydora sulcans Voigt (1965 Voigt, E. 1965. “Über parasitische Polychaeten in Kreide-Austern sowie einige andere in Muschelschalen bohrende Würmer.” Paläontologische Zeitschrift 39 (3–4): 193–211.[Crossref] , [Google Scholar]) and ?Entobia isp. attributed to endolithic bivalves, serpulid worms and clionaid sponges. Different frequencies and orientations of macroborings seen in lag deposits containing O. megalodon and O. chubutensis teeth are the result of repeated exhumation and reworking in response to bathymetrically controlled wave-based erosion during storm events and glacioeustatically driven sea-level cyclicity across Onslow Bay. Chronological ranges of O. megalodon and O. chubutensis teeth that contain macroborings indicate that these lag deposits may have been forming since the late early Miocene.     

Sciences of learning and development: Some thoughts from the learning sciences

ABSTRACT

This commentary extends and amplifies aspects of the Cantor, Osher, Berg, Steyer and Rose (2018 Cantor, P., Osher, D., Berg, J., Steyer, L., & Rose, T. (2018). Maleability, plasticity, and individuality: How children learn and develop in context. Applied Developmental Science. doi:10.1080/10888691.2017.1398649[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) discussion about what we know about the nature of learning and its implications for how we educate students across the span from early childhood through advanced levels of formal education. The paper’s overall goal is to offer some guidance and clarification about how aspects of the Cantor et al. (2018 Cantor, P., Osher, D., Berg, J., Steyer, L., & Rose, T. (2018). Maleability, plasticity, and individuality: How children learn and develop in context. Applied Developmental Science. doi:10.1080/10888691.2017.1398649[Taylor & Francis Online], [Web of Science ®] , [Google Scholar]) powerful vision of optimal and equitable development might be attained based on a view of what we mean by learning, the types of learning that matter, and ways to design environments for learning and development that allow all children to realize their potential. Three major topics are covered. The first concerns evolution of theories of learning as they relate to theories of development and the connection between the two. Emphasis is given to the power that comes from adopting a sociocultural perspective on the nature of learning and development. The second topic is a consideration of current targets of learning and development, including so-called 21^st century competencies and deep disciplinary learning. Emphasis is given to the cognitive, intrapersonal and interpersonal competency domains that integrate cognitive, affective, social and emotional processes. The third topic focuses on a set of research-based principles that can be used to design and implement powerful and equitable learning environments that align with sociocultural theories and learning and development while integrating the three major domains of competency.