Force-induced misfolding in RNA

RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of its importance in modern biophysics, the current understanding of RNA folding kinetics is limited by the complex interplay between the weak base-pair interactions that stabilize the native structure and the disordering effect of thermal forces. The possibility of mechanically pulling individual molecules offers a new perspective to understand the folding of nucleic acids. Here we investigate the folding and misfolding mechanism in RNA secondary structures pulled by mechanical forces. We introduce a model based on the identification of the minimal set of structures that reproduce the patterns of force-extension curves obtained in single molecule experiments. The model requires only two fitting parameters: the attempt frequency at the level of individual base pairs and a parameter associated to a free energy correction that accounts for the configurational entropy of an exponentially large number of neglected secondary structures. We apply the model to interpret results recently obtained in pulling experiments in the three-helix junction S15 RNA molecule (RNAS15). We show that RNAS15 undergoes force-induced misfolding where force favors the formation of a stable non-native hairpin. The model reproduces the pattern of unfolding and refolding force-extension curves, the distribution of breakage forces and the misfolding probability obtained in the experiments.Comment: 28 pages, 11 figure

Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

A two-state kinetic model for the unfolding of single molecules by mechanical force

We investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states) separated by an intermediate barrier. We compute the probability distribution for the dissipated work and give analytical expressions for the average and variance of the distribution. To first order, the amount of dissipated work is directly proportional to the rate of application of force (the loading rate), and to the relaxation time of the molecule. The model yields estimates for parameters that characterize the unfolding kinetics under force in agreement with those obtained in recent experimental results (Liphardt, J., et al. (2002) {\em Science}, {\bf 296} 1832-1835). We obtain a general equation for the minimum number of repeated experiments needed to obtain an equilibrium free energy, to within $k_BT$, from non-equilibrium experiments using the Jarzynski formula. The number of irreversible experiments grows exponentially with the ratio of the average dissipated work, \bar{\Wdis}, to $k_BT$.}Comment: PDF file, 5 page

Use of Chemical Modification To Elucidate RNA Folding Pathways

As discussed in this overview, chemical modification is sensitive to the accessibility of a nucleotide to the solvent, and many nucleotides become less accessible as an RNA folds into its structured form. Chemical modification reagents are therefore suitable for following RNA folding, and can be used to study the kinetics of structure formation on time scales ranging from minutes to hours.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143596/1/cpnc1109.pd

Use of analysis and processing of digital images for evaluation and control of animal behavior in hot climates

The world production of meats is mainly concentrated in the countries with a hot climate. Among these countries, Brazil, considered "world's breadbasket", is located in the intertropical zone, with hot climates and presents lower thermal amplitude. Brazilian poultry is a leader in the production and export of broilers. Brazil has the second largest cattle herd in the world, has the largest commercial herd besides being the largest exporter of beef. Brazilian swine breeding, among the most advanced production chains in the world, occupy the position of fourth largest producer of pork in the world. Projections for Brazil's meat production sector indicate strong growth in the coming years, with countries in hot climates that will continue to sustain future growth in world meat production, ensuring food security in many countries. One of the factors responsible for the success or failure of animal production is the environment, defined by the sum of all physical and biological factors that affect animals. In these regions of hot climates, climatic factors are among the main limiting factors to the development of animal production, which may compromise animal welfare and productivity indices. Behavioral information can aid in the analysis of problems arising from environmental conditions unfavorable to animals, helping both decision making and the use of different environmental conditioning systems. The introduction of technification in the animal behavior evaluation processes, through the use of video cameras and image processing programs, allowed a better interpretation of the behavioral responses, quickly, accurately and non-invasively, gradually being used with greater frequency in the animal production sectors. The study of animal behavior assumes an important role in animal production, since, to rationalize the breeding methods, management, feeding and facilities techniques have been developed that interfere with animal behavior. In this context, the use of digital image analysis techniques, where the animals themselves are used as biosensors in response to environmental conditions, contributes to the analysis of animal behavior, and consequently also to the assessment of the internal environment of the production in hot weather. Keywords: animal production, animal welfare, information technolog

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

TRACE ELEMENTS IN SHEEP AND GOATS REPRODUCTION: A REVIEW

The reproduction of small ruminants like goats and sheep managed under extensive range grazing conditions can be affected by nutrients availability and especially by the mineral content of the forages resources on the rangeland. It has been particularly demonstrated that trace elements can have equally, beneficial or detrimental effects, depending on its balance, on reproductive functions in small ruminants. Trace elements as copper, molybdenum, selenium and zinc play key role on the metabolism of carbohydrates, proteins and lipids; however, the mode of action by which these elements affect reproduction in sheep and goats are not completely understood, due to the complexity in the mode of action of the metallobiomolecules and the neuro-hormonal relationship. In this way, their absence or presence of these minerals in several organs, fluids, or tissues of the reproductive tract have allowed obtaining information on the metabolism and the role of these elements on reproduction in sheep and goats. On this regard, the objective of this document is to review the relationships and effects of some trace elements, on reproductive events in sheep and goats

EFFECT OF SEASON ON SERUM COPPER AND ZINC CONCENTRATIONS IN CROSSBRED GOATS HAVING DIFFERENT REPRODUCTIVE STATUS UNDER SEMIARID RANGELAND CONDITIONS IN SOUTHERN MEXICO STATE

The effect of season (rainy: RS, and dry: DS) and reproductive status on copper (Cu) and zinc (Zn) concentrations in blood serum of crossbred goats (BW= 36.01 ± 1.59 kg) were studied under semiarid rangeland conditions in Southern Mexico State. Blood samples from 80 crossbred goats were taken each season (RS and DS). The goats were clustered into 10 different groups considering their reproductive status. Concentrations of Cu and Zn in serum were assayed using atomic absorption. Data were analyzed using a general linear model procedure for a completely randomized design and differences among means were examined using a Tukey test. Blood serum concentrations of Cu and Zn were affected by reproductive status and season (P<0.001). In relation to the season, Cu and Zn serum levels were lower in RS than DS (P<0.05). Overall, kidded goats had the highest values (P<0.01) for Cu than other animals in both seasons (RS or DS). Anestrous goats had the lowest concentrations (P<0.01) for Zn during RS, while all goats at their second or more kidding, rearing single or twins, showed the highest concentrations of Zn (P<0.001) in this season. Adult goats in Southern Mexico State showed a deficiency of Cu and Zn, especially during RS. As such, mineral supplements should be provided with respect to these elements in feeding systems for goats under semiarid rangeland conditions in order to evaluate their impact on health and reproduction

An Innovative 3D Printed Tooth Reduction Guide for Precise Dental Ceramic Veneers.

Tooth reduction guides allow clinicians to obtain the ideal space required for ceramic restorations. This case report describes a novel design (CAD) for an additive computer-aided manufactured (a-CAM) tooth reduction guide with channels that permitted access for the preparation and evaluation of the reduction with the same guide. The guide features innovative vertical and horizontal channels that permit comprehensive access for preparation and evaluation of the reduction with a periodontal probe, ensuring uniform tooth reduction and avoiding overpreparation. This approach was successfully applied to a female patient with non-carious lesions and white spot lesions, resulting in minimally invasive tooth preparations and hand-crafted laminate veneer restorations that met the patient's aesthetic demands while preserving tooth structure. Compared to traditional silicone reduction guides, this novel design offers greater flexibility, enabling clinicians to evaluate tooth reduction in all directions and providing a more comprehensive assessment. Overall, this 3D printed tooth reduction guide represents a significant advancement in dental restoration technology, offering clinicians a useful tool for achieving optimal outcomes with minimal tooth reduction. Future work is warranted to compare tooth reductions and preparation time for this guide to other 3D printed guides

Diagnostic Mock-Up as a Surgical Reduction Guide for Crown Lengthening: Technique Description and Case Report.

Background and Objectives: The report describes a technique using a diagnostic mock-up as a crown-lengthening surgical guide to improve the gingival architecture. Materials and Methods: The patient's primary concern was improving her smile due to her "gummy smile" and short clinical crowns. After clinical evaluation, surgical crown lengthening accompanied by maxillary central full-coverage single-unit prostheses and lateral incisor veneers was recommended. The diagnostic mock-up was placed in the patient's maxillary anterior region and used as a soft tissue reduction guide for the gingivectomy. Once the planned gingival architecture was achieved, a flap was reflected to proceed with ostectomy in order to obtain an appropriate alveolar bone crest level using the overlay. After six months, all-ceramic crowns and porcelain veneers were provided as permanent restorations. Results: A diagnostic mock-up fabricated with a putty guide directly from the diagnostic wax-up can be an adequate surgical guide for crown-lengthening procedures. The diagnostic wax-up was used to fabricate the diagnostic mock-up. These results suggested that it can be used as a crown-lengthening surgical guide to modify the gingival architecture. Several advantages of the overlay used in the aesthetic complex case include: (1) providing a preview of potential restorative outcomes, (2) allowing for the appropriate positioning of gingival margins and the desired alveolar bone crest level for the crown-lengthening procedure, and (3) serving as a provisional restoration after surgery. Conclusions: The use of a diagnostic mock-up, which was based on a diagnostic wax-up, as the surgical guide resulted in successful crown lengthening and provisional restorations. Thus, a diagnostic overlay can be a viable option as a surgical guide for crown lengthening