Quantitative Biology

So far mutations analysis was performed in terms of transitions and trasversions, so on the basis of the molecule, or in terms of GC-content and isochors, through the quantification of GC->AT mutations over AT->GC mutations. We tried a different approach hypothesizing that probably we are partially protected (by the genetic code) from amyloid fibrils formation.

In recent years, we have witnessed a dramatic data explosion in genomics, thanks to the improvement in sequencing technologies and the drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each genome can be composed of billions of nucleotides stored as plain text files in GigaBytes (GBs). It is undeniable that those genome data impose unprecedented data challenges for us. In this article, we briefly discuss the big data challenges associated with genomics in recent years.

Two years study was carried out during 2006-07 and 2007-08 crop seasons to study the response of different genotypes of oilseeds Brassica to Lipaphis erysimi (Kaltenbach) infestation both under field and screen house conditions and to find out the relationship of various biochemical constituents to aphid infestation. Among the various genotypes, the population of L. erysimi was significantly high on Brassica rapa variety brown sarson cv. BSH 1 and B. rapa var. yellow sarson cv. YST 151 in unprotected set i.e. 53.7 and 52.3 aphids/ plant, respectively. However, it was the lowest on Eruca sativa cv. T 27 (4.7 aphids/plant) followed by B. carinata cv. DLSC 2 (20.9 aphids/ plant) which suffered the least yield loss i.e. 5.79 and 10.59 per cent, respectively. Almost similar trend was observed in seedling mortality, which was the maximum in BSH 1 and YST 151, while no seedling mortality was observed in the case of T 27 during both the years of study. Analysis of various biochemical constituents revealed that glucosinolates, total phenols and ortho-dihydroxy phenols had inverse relationship with the aphid infestation. Higher amount of these biochemical constituents in T 27 and DLSC 2 was responsible for lower aphid infestation on these genotypes.

The genetic programming of biosynthesis of biogenic magnetic nanoparticles (BMNs) in plants was revealed by methods of comparative genomics. The samples of leaves and the root of Nicotiana tabacum, the stems and tubers of Solanum tuberosum and the stems of pea Pisum sativum were examined by scanning probe microscopy (in atomic force and magnetic power modes), and it was found that the BMNs are located in the form of chains in the wall of the phloem sieve tubes (ie, the vascular tissue of plants). Such a localization of BMNs supports the idea that the chains of BMNs in different organs of plants have common metabolic functions. Stray gradient magnetic fields about several thousand Oe, which are created by chains of BMNs, can significantly affect the processes of mass transfer near the membrane of vesicles, granules, organelles, structural elements of the membrane, and others. This process is enhanced in plants when artificial magnetite is added to the soil.

A key to effective teaching is an awareness and accurate understanding of the thinking and implicit assumptions that students bring to the subject to be learned. In the absence of extensive Socratic interactions with students, one strategy to assess student thinking involves the use of concept inventories (CIs). CIs are typically multiple-choice assessments, constructed based on research into student thinking and language, and designed to reveal the presence of common misconceptions and implicit assumptions pertaining to a particular facet of a subject. Here we describe the open-source Biological Concepts Instrument (BCI), a diagnostic, multiple-choice instrument designed to provide instructors with a preliminary map of a number of basic ideas in molecular level biology. We describe the strategy behind its design, the research upon which it is based, item construction, and its possible uses as a means to reveal and address persistent and often unrecognized conceptual obstacles.

Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a pioneer of this paradigm shift from descriptive to quantitative biology not only through his numerous research accomplishments, but also through the many students and postdocs he mentored over his long career. Those of us fortunate enough to have worked with George agree that his sharp intellect, physical intuition and passion for scientific inquiry not only inspired us as scientists but also greatly influenced the way we conduct research. We would like to share a few important lessons we learned from George in honor of his memory and with the hope that they may inspire future generations of scientists.

There is evidence for the effect of blue light on circadian cycle and ocular pathologies. Moreover, the introduction of LED lamps has increased the presence of blue light. In the last two years, many different blue blocking ophthalmic lenses have been introduced. Due to the different effect of blue light on ocular media and circadian rhythm, we have defined two indices that describe the level of protection of the lenses towards the retina and the circadian cycle under different lighting as for example daylight and tablet. These indexes can help in individuating the right lens for ocular protection.

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death. Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.

We document opportunistic foraging behavior by Caiman crocodilus in a post-inundation forest at Estacíon Biologíca Caño Palma, Costa Rica.

The lyric career of Maria Callas, though exceptional, is also noteworthy for its brevity. The first signs of downturn appeared at the age of 36 and her voice fell silent at only 40. Though the literature has massively commented on this premature worsening, few analyses of its characteristics have been made public so far. The purpose of our study was to realise a perceptual and acoustical analysis of recorded arias by the artist at the climax to the fall. The audible impairments were first verbally described, and then compared to acoustical observations based on spectrographic analyses and fundamental-frequency measurements.