Novel hybrid encodes both continuous and split tRNA genes?

tRNAs are mostly transcribed from un-fragmented genes, but occasionally also from split genes, with separated 5' and 3' halves. A reanalysis of the existing data on Staphylothermus marinus and Staphylothermus hellenicus hints of a novel hybrid gene that encodes both an un-fragmented and a 5'-split-half together in one. The corresponding 3' complement-gene is located elsewhere on the genome. As un-fragmented, the hybrid gene transcribes to tRNA(lys)(TTT). But as 5'-half, it trans-splices with its 3'-complement-half to tRNA(lys)(CTT), the tRNA missed so far. This hybrid of the split and the un-fragmented in one suggests a deeper synergy between the two, and hints of co-evolution. Furthermore, in a subtle contrast to the widely held idea of conservation of 3'-half, it is precisely the 3'-half that varies in these two tRNAs; the 5'-half remains conserved.     

In silico modeling of pH-optimum of protein-protein binding

Protein-protein association is a pH-dependent process and thus the binding affinity depends on the local pH. In vivo the association occurs in a particular cellular compartment, where the individual monomers are supposed to meet and form a complex. Since the monomers and the complex exist in the same micro environment, it is plausible that they coevolved toward its properties, in particular, toward the characteristic subcellular pH. Here we show that the pH at which the monomers are most stable (pH-optimum) or the pH at which stability is almost pH-independent (pH-flat) of monomers are correlated with the pH-optimum of maximal affinity (pH-optimum of binding) or pH interval at which affinity is almost pH-independent (pH-flat of binding) of the complexes made of the corresponding monomers. The analysis of interfacial properties of protein complexes demonstrates that pH-dependent properties can be roughly estimated using the interface charge alone. In addition, we introduce a parameter beta, proportional to the square root of the absolute product of the net charges of monomers, and show that protein complexes characterized with small or very large beta tend to have neutral pH-optimum. Further more, protein complexes made of monomers carrying the same polarity net charge at neutral pH have either very low or very high pH-optimum of binding. These findings are used to propose empirical rule for predicting pH-optimum of binding provided that the amino acid compositions of the corresponding monomers are available.     

Radial distance determination in the rat vibrissal system and the effects of Weber's law

Rats rhythmically tap and brush their vibrissae (whiskers) against objects to tactually explore the environment. To extract a complex feature such as the contour of an object, the rat must at least implicitly estimate radial object distance, that is, the distance from the base of the vibrissa to the point of object contact. Radial object distance cannot be directly measured, however, because there are no mechanoreceptors along the vibrissa. Instead, the mechanical signals generated by the vibrissa's interaction with the environment must be transmitted to mechanoreceptors near the vibrissa base. The first part of this paper surveys the different mechanical methods by which the rat could determine radial object distance. Two novel methods are highlighted: one based on measurement of bending moment and axial force at the vibrissa base, and a second based on measurement of how far the vibrissa rotates beyond initial contact. The second part of the paper discusses the application of Weber's law to two methods for radial distance determination. In both cases, Weber's law predicts that the rat will have greatest sensing resolution close to the vibrissa tip. These predictions could be tested with behavioural experiments that measure the perceptual acuity of the rat.     

Identifying polyglutamine protein species in situ that best predict neurodegeneration

Polyglutamine (polyQ) stretches exceeding a threshold length confer a toxic function to proteins that contain them and cause at least nine neurological disorders. The basis for this toxicity threshold is unclear. Although polyQ expansions render proteins prone to aggregate into inclusion bodies, this may be a neuronal coping response to more toxic forms of polyQ. The exact structure of these more toxic forms is unknown. Here we show that the monoclonal antibody 3B5H10 recognizes a species of polyQ protein in situ that strongly predicts neuronal death. The epitope selectively appears among some of the many low-molecular-weight conformational states assumed by expanded polyQ and disappears in higher-molecular-weight aggregated forms, such as inclusion bodies. These results suggest that protein monomers and possibly small oligomers containing expanded polyQ stretches can adopt a conformation that is recognized by 3B5H10 and is toxic or closely related to a toxic species.     

Providing Spark and Stability: The Role of Intermediary Organizations in Establishing School-Based Youth-Adult Partnerships

The term “youth-adult partnership” increasingly is being used to define a relationship in which both youth and adults have the potential to contribute to decision making processes, to learn from one another, and to promote change. Establishing a relationship with an intermediary organization can provide much needed stability and sustainability to youth-adult partnerships–especially in school settings. Rather than creating generalizable findings, this article focuses on hypothesis generation regarding the ways in which an intermediary organization can provide the needed training and support to school-based youth-adult partnerships. Using a combination of case-study and survey data, the study finds that youth-adult partnerships need help with: youth leadership skill development, team building, project development, and targeted training for adults. Technical assistance needs vary depending on whether groups need to create a spark that will build the idea of a youth-adult partnership or to create stability for a youth-adult partnership that has already been developed     

Enhancing the Strength of an Optical Trap by Truncation

Optical traps (tweezers) are beginning to be used with increasing efficacy in diverse studies in the biological and biomedical sciences. We report here results of a systematic study aimed at enhancing the efficiency with which dielectric (transparent) materials can be optically trapped. Specifically, we investigate how truncation of the incident laser beam affects the strength of an optical trap in the presence of a circular aperture. Apertures of various sizes have been used by us to alter the beam radius, thereby changing the effective numerical aperture and intensity profile. We observe significant enhancement of the radial and axial trap stiffness when an aperture is used to truncate the beam compared to when no aperture was used, keeping incident laser power constant. Enhancement in trap stiffness persists even when the beam intensity profile is modulated. The possibility of applying truncation to multiple traps is explored; to this end a wire mesh is utilized to produce multiple trapping that also alters the effective numerical aperture. The use of a mesh leads to reduction in trap stiffness compared to the case when no wire mesh is used. Our findings lead to a simple-to-implement and inexpensive method of significantly enhancing optical trapping efficiency under a wide range of circumstances.     

Computational discovery of soybean promoter cis‐regulatory elements for the construction of soybean cyst nematode‐inducible synthetic promoters

Computational methods offer great hope but limited accuracy in the prediction of functional cis‐regulatory elements; improvements are needed to enable synthetic promoter design. We applied an ensemble strategy for de novo soybean cyst nematode (SCN)‐inducible motif discovery among promoters of 18 co‐expressed soybean genes that were selected from six reported microarray studies involving a compatible soybean–SCN interaction. A total of 116 overlapping motif regions (OMRs) were discovered bioinformatically that were identified by at least four out of seven bioinformatic tools. Using synthetic promoters, the inducibility of each OMR or motif itself was evaluated by co‐localization of gain of function of an orange fluorescent protein reporter and the presence of SCN in transgenic soybean hairy roots. Among 16 OMRs detected from two experimentally confirmed SCN‐inducible promoters, 11 OMRs (i.e. 68.75%) were experimentally confirmed to be SCN‐inducible, leading to the discovery of 23 core motifs of 5‐ to 7‐bp length, of which 14 are novel in plants. We found that a combination of the three best tools (i.e. SCOPE, W‐AlignACE and Weeder) could detect all 23 core motifs. Thus, this strategy is a high‐throughput approach for de novo motif discovery in soybean and offers great potential for novel motif discovery and synthetic promoter engineering for any plant and trait in crop biotechnology.     

Synthesis, characterization, electrochemical and magnetic studies on manganese(III) complexes involving bridging carboxylates

A series of carboxylate-bridged manganese(III) complexes derived from Schiff bases obtained by the condensation of salicylaldehyde or 5-bromo-salicylaldehyde and different types of diamine have been synthesized and characterized and, in the case of [Mn₂(L1)₂(μ-ClCH₂COO)](ClO₄) (1), the structure has been obtained by X-ray crystallography. The structure of 1 consists of two manganese atoms separated by 5.487(3) Å and bridged by a carboxylate anion. This dinuclear structural unit is linked by bridging phenoxy oxygens to adjacent dinuclear units to produce a one-dimensional chain. Cyclic voltammograms of all the compounds exhibit grossly similar features consisting of a reversible or quasi-reversible Mn^III/Mn^II reduction and a Mn^III/Mn^IV oxidation. It has been observed that bromo-substitution stabilizes the lower oxidation state in the Mn^III/Mn^II couple and destabilizes the higher oxidation state in the Mn^III/Mn^IV couple. Variable temperature magnetic susceptibility measurements of 1 show a weak antiferromagnetic interaction. The magnetic behavior is satisfactorily modeled by inclusion of zero-field splitting and an intermolecular interaction component.     

Structural basis of recognition of pathogen-associated molecular patterns and inhibition of proinflammatory cytokines by camel peptidoglycan recognition protein

Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated molecular patterns. The well known pathogen-associated molecular patterns include LPS from Gram-negative bacteria and lipoteichoic acid (LTA) from Gram-positive bacteria. In this work, the crystal structures of two complexes of the short form of camel PGRP (CPGRP-S) with LPS and LTA determined at 1.7- and 2.1-? resolutions, respectively, are reported. Both compounds were held firmly inside the complex formed with four CPGRP-S molecules designated A, B, C, and D. The binding cleft is located at the interface of molecules C and D, which is extendable to the interface of molecules A and C. The interface of molecules A and B is tightly packed, whereas that of molecules B and D forms a wide channel. The hydrophilic moieties of these compounds occupy a common region, whereas hydrophobic chains interact with distinct regions in the binding site. The binding studies showed that CPGRP-S binds to LPS and LTA with affinities of 1.6 × 10(-9) and 2.4 × 10(-8) M, respectively. The flow cytometric studies showed that both LPS- and LTA-induced expression of the proinflammatory cytokines TNF-α and IL-6 was inhibited by CPGRP-S. The results of animal studies using mouse models indicated that both LPS- and LTA-induced mortality rates decreased drastically when CPGRP-S was administered. The recognition of both LPS and LTA, their high binding affinities for CPGRP-S, the significant decrease in the production of LPS- and LTA-induced TNF-α and IL-6, and the drastic reduction in the mortality rates in mice by CPGRP-S indicate its useful properties as an antibiotic agent.     

Synthesis, structure and theoretical studies of Hg(II)-NH carbene complex of annulated ligand pyridinyl[1,2-a]{2-pyridylimidazol}-3-ylidene hexaflurophosphate

Experimental and theoretical studies of a new class of novel annulated imidazolium scffords 2a, 2b, 2c and their Hg(II)-NHC complexes 3a, 3b and 3c have been synthesized and characterized by different spectroscopic techniques. Molecular structures of 3a and 3b have been determined by single crystal X-ray diffraction studies. Virtual linear geometry [C_carbene-Hg-C_carbene 176.56(17)°] around Hg of the complex 3b is observed where as in 3a and 3c its deviate a more. DFT calculations provide geometrical parameters in conformity with the experimental values in case of 3a. The molecules prefer syn configuration over the anti due to lower energy supported by theoretical studies. Attention has given paid for theoretical calculations and comparison of 3a and 3c to observe the steric effect of -CH₃ group in the scaffords where as in case of 3b the -CH₃ group remain innocent.