Towards a theory of meaning in biology: a proposal for an operative definition.

Information is a concept developed inside the context of computational and computer sciences. Entropy is a concept developed inside physics context. The best concept in biology is that of "meaning" which is quite impossible to be measured as stated by some examples which are reported. A suggestion to develop a discussion in order to obtain an integration of these concepts inside the general problems of evolutionary biology is here reported to the attention of researchers.     

Cell death in Pseudomonas aeruginosa biofilm development

Bacteria growing in biofilms often develop multicellular, three-dimensional structures known as microcolonies. Complex differentiation within biofilms of Pseudomonas aeruginosa occurs, leading to the creation of voids inside microcolonies and to the dispersal of cells from within these voids. However, key developmental processes regulating these events are poorly understood. A normal component of multicellular development is cell death. Here we report that a repeatable pattern of cell death and lysis occurs in biofilms of P. aeruginosa during the normal course of development. Cell death occurred with temporal and spatial organization within biofilms, inside microcolonies, when the biofilms were allowed to develop in continuous-culture flow cells. A subpopulation of viable cells was always observed in these regions. During the onset of biofilm killing and during biofilm development thereafter, a bacteriophage capable of superinfecting and lysing the P. aeruginosa parent strain was detected in the fluid effluent from the biofilm. The bacteriophage implicated in biofilm killing was closely related to the filamentous phage Pf1 and existed as a prophage within the genome of P. aeruginosa. We propose that prophage-mediated cell death is an important mechanism of differentiation inside microcolonies that facilitates dispersal of a subpopulation of surviving cells.     

Ion-dependent DNA configuration in bacteriophage capsids

Bacteriophages densely pack their long double-stranded DNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of the hexagonal packing depend on the electrochemistry of the capsid and its environment. In this work, we propose a biophysical model that quantifies the relationship between DNA configurations inside bacteriophage capsids and the types and concentrations of ions present in a biological system. We introduce an expression for the free energy that combines the electrostatic energy with contributions from bending of individual segments of DNA and Lennard-Jones-type interactions between these segments. The equilibrium points of this energy solve a partial differential equation that defines the distributions of DNA and the ions inside the capsid. We develop a computational approach that allows us to simulate much larger systems than what is possible using the existing molecular-level methods. In particular, we are able to estimate bending and repulsion between the DNA segments as well as the full electrochemistry of the solution, both inside and outside of the capsid. The numerical results show good agreement with existing experiments and with molecular dynamics simulations for small capsids.     

伊贝母体细胞无性系的建立及其胚状体的发生

本文报道了伊贝母体细胞无性系的建立及其胚状体的发生。已继代培养三年零六个月共30多代的鳞芽愈伤组织,目前仍有分化能力。通过愈伤组织形态细胞学的观察,发现伊贝母体细胞无性系形成小鳞茎的途径有二:一是由特化了的愈伤组织表皮细胞。经多次分裂发育成不定芽而形成小鳞茎;二是由愈伤组织表层或内层特化了的胚性细胞,经多次分裂发育成胚状体而形成小鳞茎。不定芽和胚状体的形态发生是有区别的。     

Hymenolepis diminuta utilizes the envelope surrounding Moniliformis moniliformis in order to survive in the cockroach host

The acanthocephalan Moniliformis moniliformis is surrounded by a membranous envelope that protects the parasite from hemocytic attack in the cockroach host. If injected into a cockroach infected with M. moniliformis, hatched oncospheres of the tapeworm Hymenolepis diminuta are able to penetrate this envelope and, once inside, utilize its protective function in order to develop. These "double parasites" were infective to rats.     

Mesenchymal stem cell cultivation in electrospun scaffolds: mechanistic modeling for tissue engineering

Tissue engineering is a multidisciplinary field of research in which the cells, biomaterials, and processes can be optimized to develop a tissue substitute. Three-dimensional (3D) architectural features from electrospun scaffolds, such as porosity, tortuosity, fiber diameter, pore size, and interconnectivity have a great impact on cell behavior. Regarding tissue development in vitro, culture conditions such as pH, osmolality, temperature, nutrient, and metabolite concentrations dictate cell viability inside the constructs. The effect of different electrospun scaffold properties, bioreactor designs, mesenchymal stem cell culture parameters, and seeding techniques on cell behavior can be studied individually or combined with phenomenological modeling techniques. This work reviews the main culture and scaffold factors that affect tissue development in vitro regarding the culture of cells inside 3D matrices. The mathematical modeling of the relationship between these factors and cell behavior inside 3D constructs has also been critically reviewed, focusing on mesenchymal stem cell culture in electrospun scaffolds.     

The odontode explosion: The origin of tooth‐like structures in vertebrates

Essentially we show recent data to shed new light on the thorny controversy of how teeth arose in evolution. Essentially we show (a) how teeth can form equally from any epithelium, be it endoderm, ectoderm or a combination of the two and (b) that the gene expression programs of oral versus pharyngeal teeth are remarkably similar. Classic theories suggest that (i) skin denticles evolved first and odontode‐inductive surface ectoderm merged inside the oral cavity to form teeth (the ‘outside‐in’ hypothesis) or that (ii) patterned odontodes evolved first from endoderm deep inside the pharyngeal cavity (the ‘inside‐out’ hypothesis). We propose a new perspective that views odontodes as structures sharing a deep molecular homology, united by sets of co‐expressed genes defining a competent thickened epithelium and a collaborative neural crest‐derived ectomesenchyme. Simply put, odontodes develop ‘inside and out’, wherever and whenever these co‐expressed gene sets signal to one another. Our perspective complements the classic theories and highlights an agenda for specific experimental manipulations in model and non‐model organisms.     

LISP1 is important for the egress of Plasmodium berghei parasites from liver cells

Most Apicomplexa are obligatory intracellular parasites that multiply inside a so-called parasitophorous vacuole (PV) formed upon parasite entry into the host cell. Plasmodium , the agent of malaria and the Apicomplexa most deadly to humans, multiplies in both hepatocytes and erythrocytes in the mammalian host. Although much has been learned on how Apicomplexa parasites invade host cells inside a PV, little is known of how they rupture the PV membrane and egress host cells. Here, we characterize a Plasmodium protein, called LISP1 ( li ver- s pecific p rotein 1), which is specifically involved in parasite egress from hepatocytes. LISP1 is expressed late during parasite development inside hepatocytes and locates at the PV membrane. Intracellular parasites deficient in LISP1 develop into hepatic merozoites, which display normal infectivity to erythrocytes. However, LISP1-deficient liver-stage parasites do not rupture the membrane of the PV and remain trapped inside hepatocytes. LISP1 is the first Plasmodium protein shown by gene targeting to be involved in the lysis of the PV membrane.     

The parasitophorous vacuole membrane of Encephalitozoon cuniculi lacks host cell membrane proteins immediately after invasion

Microsporidia of the genus Encephalitozoon develop inside a parasitophorous vacuole (PV) of unknown origin. Using colocalization studies, the PV was found to be absent from the endocytic pathway markers early endosomal autoantigen 1, transferrin receptor, and lysosome-associated membrane protein 1 and for the endoplasmic reticulum marker calnexin. The nonfusiogenic characteristic of the PV appears to be acquired as early as 1 min postinfection and is not reversed by drug treatment with albendazole or fumagillin.     

Larval legs of mulberry silkworm Bombyx mori are prototypes for the adult legs

Morphological diversity of leg appendages is one of the hallmarks of developmental evolution. Limbs in insects may develop either from their embryonic prototypes or from imaginal discs harbored inside the larva. Bombyx mori (B. mori), a Lepidopteran insect, develops adult wings from larval wing imaginal discs. However, it has been debated whether the adult legs of B. mori arise from imaginal discs or from the larval legs. Here we addressed how the larval legs relate to their adult counterparts. We present the morphological landmarks during early leg development. We used expression of developmental genes like Distalless and extradenticle to mark leg primordia. Finally, we employed classical excision approach to develop a fate map of the adult leg. Excision and ablation of thoracic legs along proximo-distal axis at various times during larval development resulted in the loss of corresponding adult leg segments. Our data suggest that B. mori legs develop from larval appendages rather than leg imaginal discs.     

The effect of controlled growth factor delivery on embryonic stem cell differentiation inside fibrin scaffolds

The goal of this project was to develop 3-D biomaterial scaffolds that present cues to direct the differentiation of embryonic stem (ES) cell-derived neural progenitor cells, seeded inside the scaffolds, into mature neural phenotypes, specifically neurons and oligodendrocytes. Release studies were performed to determine the appropriate conditions for retention of neurotrophin-3 (NT-3), sonic hedgehog, and platelet-derived growth factor (PDGF) by an affinity-based delivery system incorporated into fibrin scaffolds. Embryoid bodies containing neural progenitors were formed from mouse ES cells, using a 4−/4+ retinoic acid treatment protocol, and then seeded inside fibrin scaffolds containing the drug delivery system. This delivery system was used to deliver various growth factor doses and combinations to the cells seeded inside the scaffolds. Controlled delivery of NT-3 and PDGF simultaneously increased the fraction of neural progenitors, neurons, and oligodendrocytes while decreasing the fraction of astrocytes obtained compared to control cultures seeded inside unmodified fibrin scaffolds with no growth factors present in the medium. These results demonstrate that such a strategy can be used to generate an engineered tissue for the potential treatment of spinal cord injury and could be extended to the study of differentiation in other tissues.     

The development of the tuber in seedlings of five species of Dioscorea from Nigeria

Tubers in all five species develop from the hypocotyl region of the seedlingS. A perivascular cambium arises cutting off mainly starch-storing parenchyma and collateral vascular bundles to the inside. A phellogen gives rise to cork on the outside. Between the two cambial layers there may or may not be layers of parenchyma, not storing starch but containing raphides. The vascular bundles consist of xylem with vessels, scalariform tracheids and parenchyma; and phloem, with sieve tubes and parenchyma.     

PHIALIDE AND CONIDIUM DEVELOPMENT IN ASPERGILLUS CLAVATUS

Phialide formation in Aspergillus clavatus begins with the formation of thin areas in the vesicle wall. These thin-walled regions and adjacent cytoplasm then push out synchronously to produce the phialides. Mature phialides are broadly oval with an attenuated base and tapered apex. A secondary wall forms inside the phialide apex. The entire phialide apex pushes out to form the first conidium which is delimited by formation of a septum inside the mouth of the phialide. No collarette is present as the first conidium forms, but as the second conidium begins to develop, the outer wall breaks at the mouth of the phialide, leaving a collarette. The walls of the second and subsequent conidia are continuous with the inner wall of the phialide apex, from which they form. Conidia are held in chains by a connective which is a greatly thickened septum.     

The parasitic nematode Phasmarhabditis hermaphrodita defends its slug host from being predated or scavenged by manipulating host spatial behaviour

Infective stages of commercially used molluscicidal rhabditide nematodes Phasmarhabditis hermaphrodita contain bacterial symbionts which kill their host by septicaemia. The nematodes feed on the multiplying bacteria and entire host tissue, develop and repeatedly reproduce. Invertebrate cadavers are rapidly (from minutes to hours) removed by scavengers. However nematodes need days to complete their life cycle inside the host.

The post mortem locations of slugs killed by six different treatments (three types of molluscicides, a simulation of unsuccessful predation and two P. hermaphrodita nematode treatments) were compared.

In comparison to other pathogenic states, significantly more slugs killed by the nematodes died within the soil, where the scavenging pressure is weaker than on the soil surface (where most of the slugs died regardless treatment). We suggest that this is an outcome of behavioural manipulation, which prevent the parasites from being predated or scavenged together with their host until the nematodes complete development inside the host cadaver.     

Protective role of cisplatin in ischemic liver injury through induction of autophagy

High mobility group box 1 (HMGB1) is a nuclear protein released from stressed or damaged cells that activates inflammatory cascades involved in the pathogenesis of liver ischemia reperfusion (I/R) injury. In efforts to develop strategies aimed at preventing its release from ischemic cells following I/R, we studied the use of cisplatin, a member of the platinating chemotherapeutic agents capable of inducing DNA lesions that have high binding affinities for high mobility group proteins inside the nucleus of cells. In addition to demonstrating that cisplatin can prevent liver damage associated with liver I/R by sequestering HMGB1 inside the nucleus of ischemic cells, cisplatin can also alter cell survival signaling through autophagy. Our results provide a potential approach involving the use of platinating agents and their effects on autophagy in mitigating the deleterious effects of ischemia reperfusion-mediated disease processes.     

Dwarf male of Symbion pandora (cycliophora)

This study clarifies the identity and development of the male in the life cycle of Symbion pandora. The male is not produced directly by the feeding stage, as previously thought, but arises as a distinct individual from budding cells inside an intermediate stage named the Prometheus larva. The morphology and the development of the two distinct stages are described with light and electron microscopy. Furthermore, the following terminology is suggested to clearly distinguish between the different individuals: 1) the Prometheus larva, which is the free-swimming individual being produced inside the feeding stage; 2) the attached Prometheus larva on the feeding stage, which mostly degenerates following settlement, except for the internal budding cells; and 3) the dwarf male, which is the ciliated, sexually mature stage. The budding cells inside the attached Prometheus larva usually develop two internal dwarf males. Each dwarf male is heavily ciliated and has a well-developed nervous system with a relatively large brain, numerous gland and muscle cells, testis with bundles of sperm, and one penial structure. The male lacks a gut, as in the other free stages in the life cycle of Symbion pandora. This study also indicates that the dwarf male is freed from the attached Prometheus larva. Copulation, which has not been observed yet, probably takes place between a free-swimming male and the female, either while the female is released or afterwards.     

Thymic alterations in Plasmodium berghei-infected mice

The primary function of the thymus is to develop immature T-cells into cells that further in the periphery will be able to carry out immune functions. The Literature has shown that thymus can be a target for many pathogens and severe structural alterations take place in this organ during infectious diseases. Here, we investigated if thymus is also a target organ during experimental malaria infection by analyzing the presence of parasites inside the organ and histological alterations in thymuses from Plasmodium berghei NK65-infected BALB/c. After 14 days of infection, parasites were found inside the thymus that presented a profound atrophy with total loss of its architecture. We propose that the presence of parasites in the thymus induces histological modifications that alter the microenvironment, impairing by consequence the successful T cell development. Additional studies are currently being developed in our laboratory to verify if such thymic alterations can influence the systemic immune response to the parasite.     

Superporous IPN hydrogels having enhanced mechanical properties

The objective of this study was to improve the mechanical properties of superporous hydrogels (SPHs), which were used to develop gastric retention devices for long-term oral drug delivery. The main approach used in this study was to form an interpenetrating polymer network by incorporating a second polymer network inside an SPH structure. Polyacrylonitrile was used as the second network inside an SPH. Mechanical properties including compression strength and elasticity were significantly improved, up to 50 times as compared with the control SPHs. The enhanced mechanical properties were a result of the scaffold-like fiber network structures formed inside the cell walls of SPHs. The fast swelling property of SPHs was not affected by the incorporation of the second polymer network because the interconnected pore structures were maintained. Gastric retention devices based on superporous IPN hydrogels (SPIHs) with the improved mechanical properties are expected to withstand compression pressure and mechanical frictions in the stomach better than the control SPHs.     

Growth of Preimplatation Bovine Embryos

Development of mammalian embryos in vitro is functionally and temporally inferior to embryo development as it occurs inside the female reproductive tract. The deficiencies of cultured embryos range from slow cleavage rates to complete developmental arrests or blocks, occurring at particular stages in many species. A variety of approaches have been used to overcome the blocks, including most extensively the coculture of preimplantation embryos with various somatic cells. However, even with coculture, development of embryos in vitro is still not equivalent to that in vivo. In most laboratories, only 25–40% of inseminated oocytes develop into morulae and blastocysts in spite of numerous variations on the basic technique. A better understanding of the factors governing embryonic growth is required before we can hope to achieve results comparable with those occurring in vivo.