randtip, a generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. Here, we present a completely generalized and flexible framework to expand incomplete molecular phylogenies. The framework is implemented in the R package "randtip", a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip is capable of automatically generating fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the "blind" expansion of phylogenies (using randtip or any other available software) often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step workflow. Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete molecular phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses.

Functionalised Nanopores: Chemical and Biological Modifications

Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information...

Effects of electrically transferred molecular information on the germination of garden cress

We followed a hypothesis that biologically relevant information from various substances can be non-chemically transferred to organisms through a combination of a high voltage electric field that can stably imprint information into water or a water solution. A special device was constructed, and a thoroughly tested biological sensor system (i.e. cress seedlings exposed to a defined heat stress), was used. The results demonstrate a clear evidence of biological effects of electrically imprinted information of biologically active substances into water solution, however not necessarily with an obvious connection to the effects of the original (donor) substance. The growth reaction of cress seedlings was either stimulatory or inhibitory, depending on the time of the application. Keywords: Molecular information, electromagnetic transfer, heat stress, herbicide, cytokine, cress, germination. Efeitos de informação molecular transferida eletricamente sobre a germinação do agrião Resumo Seguimos a hipótese de que informação biologicamente relevante de várias substâncias pode ser transferida de maneira não química a organismos, através da combinação de um campo elétrico de alta intensidade, que pode imprimir estavelmente informação na água ou sistemas aquosos. Foi construído um aparelho especial e foi utilizado um sistema sensor especial, amplamente provado (plantas de agrião expostas a estresse térmico definido). Os resultados demonstram evidéncia dos efeitos de informação eletricamente impressa de substâncias biologicamente ativas em soluções aquosas. No entanto, estes efeitos não estão necessariamente ligados aos próprios da substância original (doadora). A reação de crescimento das plantas de agrião foi ora estimulatória ou inibidora, dependendo do momento da aplicação. Palavras-chave: Informações moleculares, transferéncias electromagnéticos, estresse térmico, herbicida, citocinas, agrião, germinação. Efectos de información molecular transferida eléctricamente sobre la germinación de berro Resumen Seguimos la hipótesis de que información biológicamente relevante de varias sustancias puede ser transferida de modo no químico a organismos mediante la combinación de un campo eléctrico de alto voltaje que puede imprimir establemente información en el agua o soluciones acuosas. Un aparato especial fue construído y un sistema sensor ampliamente probado (mudas de berro expuestas a stress térmico definido) fie utilizado. Los resultados demuestran clara evidencia de los efectos de información eléctricamente impresa de sustancias biológicamente activas en soluciones acuosas, sin embargo, estos efectos no están necesariamente asociados con los propios de la sustancia original (donante). La reacción de crecimiento de las mudas de berro fue estimuladora o inhibidora dependiendo del horario de aplicación. Palabras-clave: Información molecular, transferencias electromagnéticas, estrés térmico, herbicidas, citoquinas, germinacion. Correspondence author: Romana Ruzic, [email protected] How to cite this article: Ruzic R, Jerman I, Skarja M, Leskovar RT, Mogilnicki L. Electromagnetic transference of molecular information in garden cress germination. Int J High Dilution Res [online]. 2008 [cited YYYY Mmm DD]; 7(24): 122-131. Available from: http://journal.giri-society.org/index.php/ijhdr/article/view/300/366.

Biosemiotics and Body Signifier Theory: a way to understand High Dilutions

Since the 80´s Madeleine Bastide and Agnès Lagache have worked on the idea of the Body Signifier Theory, in which the living systems could be defined as “sensible” systems not only able to self-organize, but also to receive and process non-molecular information according to the Pierce semiotic triad: matrix, receiver and carrier. These ideas were built along 20 years of experimental observations, whose results presented some kind of stereotyped pattern that emerged from cells or animals exposed to high dilutions, according to the similia principle. Curiously, at the same time, classical scientific communities have developed the concept of biosemiotics after the observation that living systems are semiotics entities able to deal with codes and meanings, even in molecule-driven processes. Not only the genetic code, but all regulatory functions in living systems represent coding processes. The development of methodologies to identify and understand these codes and its outputs is the aim of biosemiotic science. Putting both concepts together (body signifiers and biosemiotics), it is possible to recognize strong similarities between their approaches and methodology, allowing logical connections between non-molecular signals and changes in cell interactions patterns. Thus, the general concept of biosemiotic could be a theoretical platform on which the construction of a solid phenomenological description of high dilutions effects could be done.

Characterization of Wild Rice - Oryza Species Complexes in Sri Lanka

Rice is the staple food crop in Sri Lanka, which occupies 34% (0.77/million ha) of the total cultivated area. Sri Lanka currently produces 2.7 million tonnes of rough rice annually and satisfies around 95% of the domestic requirement. In Sri Lanka, genus Oryza consists of two species complexes, O. sativa (AA) and O. officinalis (CC). These two complexes are both pan tropical and have very similar overall distribution. Five wild rice species are reported in Sri Lanka, (O. nivara [AA], O. rufipogan (AA) O. eichengeri [CC], O. rhizomatis (CC) and O. granulate (GG). O. rhizomatis has been reported only in Sri Lanka and considered endemic to Sri Lanka. Recent studies demonstrated, the reliance on single source of information could mislead results in the phylogenetic inferences due to analytical inconsistency and biological processes. Therefore, exact number of wild rice species in Sri Lanka becomes uncertain and the necessity arises to assess Oryza species complexes in Sri Lanka using morphological, anatomical, and molecular information to enumerate number of species within each Oryza complex and characterization of species and species complexes. The study revealed, characterization of wild rice species, to a certain extent, can be made through morphological and anatomical characters, specially lamina anatomical characters. Molecular information is more reliable in delimitation of wild rice species complexes in Sri Lanka. O. rhizomatis and O. eichingeri (CC) are well separated from the rest of wild rice species (AA). Molecular data revealed, O. nivara and O. rufipogon have undergone independent evolution within Sri Lanka. Well separated five wild rice species are existing in Sri Lanka. Studies on ecological resilience of morphological, anatomical, and molecular studies are very useful for species enumeration of wild rice complexes in Sri Lanka. The findings led to conclude that wild rice species in Sri Lanka are “ecological swarms” and represents allopatric or sympatric populations. A comprehensive knowledge on genetic diversity and population structure of wild rice germplasm in Sri Lanka provides useful information to include these locally adapted and evolved wild rice species in rice crop improvement/breeding.

Updates on Molecular Targeted Therapies for Intraparenchymal CNS Metastases

Central nervous system (CNS) metastases can occur in a high percentage of systemic cancer patients and is a major cause of morbidity and mortality in these patients. Almost any histology can find its way to the brain, but lung, breast, and melanoma are the most common pathologies seen in the CNS from metastatic disease. Identification of many key targets in the tumorigenesis pathway has been crucial to the development of a number of drugs that have demonstrated successful penetration of the blood–brain, blood–cerebrospinal fluid, and blood–tumor barriers. Targeted therapy and immunotherapy have dramatically revolutionized the field with treatment options that can provide successful and durable control of even CNS disease. In this review, we discuss major targets with successful treatment options as demonstrated in clinical trials. These include tyrosine kinase inhibitors, monoclonal antibodies, and antibody–drug conjugates. We also provide an update on the state of the field and highlight key upcoming trials. Patient-specific molecular information combined with novel therapeutic approaches and new agents has demonstrated and continues to promise significant progress in the management of patients with CNS metastases.

Rehydration of freeze substituted brain tissue for preembedding immuno-electron microscopy

Electron microscopy (EM) volume reconstruction is a powerful tool for investigating the fundamental structure of brain circuits, but the full potential of this technique is limited by the difficulty of integrating molecular information. High quality ultrastructural preservation is necessary for EM reconstruction, and intact, highly contrasted cell membranes are essential for following small neuronal processes through serial sections. Unfortunately, the antibody labeling methods used to identify most endogenous molecules result in compromised morphology, especially of membranes. Cryofixation can produce superior morphological preservation and has the additional advantage of allowing indefinite storage of valuable samples. We have developed a method based on cryofixation that allows sensitive immunolabeling of endogenous molecules, preserves excellent ultrastructure, and is compatible with high-contrast staining for serial EM reconstruction.

Nanostructure-enhanced infrared spectroscopy

While infrared spectroscopy is a powerful technique that provides molecular information such as chemical constituents and chemical structures of analytes, it suffers from low absorption cross-section resulting in low sensitivity and poor signal-to-noise or signal-to-background ratios. Surface-enhanced infrared absorption (SEIRA) spectroscopy, which is supported by nanometer scale structures, is a promising technology to overcome these problems in conventional infrared (IR) spectroscopy and enhances IR signals using the field enhancement properties of surface plasmon resonance. Recently resonant SEIRA technique was proposed, and signal enhancement factor was significantly improved. In this review, we present an overview of the recent progresses on resonant SEIRA technologies including nanoantenna- and metamaterial-based SEIRA, and also SEIRA techniques with nanoimaging capabilities.