Scoring functions in protein folding and design

We present an analysis of the assumptions behind some of the most commonly used methods for evaluating the goodness of the fit between a sequence and a structure. Our studies on a lattice model show that methods based on statistical considerations are easy to use and can capture some of the features of protein-like sequences and their corresponding native states, but unfortunately are incapable of recognizing, with certainty, the native-like conformation of a sequence among a set of decoys. Meanwhile, an optimization method, entailing the determination of the parameters of an effective free energy of interaction, is much more reliable in recognizing the native state of a sequence. However, the statistical method is shown to perform quite well in tests of protein design.     

Inter-simple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters

 We describe a simple and new approach, based on inter-simple sequence repeats (ISSRs), for finding markers linked to clusters of disease resistance genes. In this approach, simple sequence repeats (SSR) are used directly in PCR reactions, and markers found to be linked to disease resistance genes provide important information for the selection of other sequences which can be used with PCR to find other linked markers. Based on an ISSR marker linked to a gene of interest, many new markers can be identified in the same region. We previously demonstrated that ISSR markers are useful in gene tagging and identified a marker, UBC-855₅₀₀, linked to the gene for resistance to fusarium wilt race 4 in chickpea. This ISSR marker provided the information used in the present study for selecting other primers which amplified a region linked to the gene for resistance to fusarium wilt race 4. The primers were based on homology with the (AC)_n sequence and were used for PCR amplifications. Changes in the sequence were at the anchor region of the primers. The repeat (AC)₈T amplified a marker, UBC-825₁₂₀₀, which was located 5.0 cM from the gene for resistance to fusarium wilt race 4 and was closer than other markers. These results indicated that ISSR markers can provide important information for the design of other primers and that by making changes at the 3′ and 5′ anchors close linkage to the desired gene can be found. The approach allows rapid scanning of the targeted region and may provide important information for genome analysis of plant species. Received: 20 January 1998 / Accepted: 19 March 1998     

Comparison of 15N- and 13C-determined parameters of mobility in melittin

Backbone and tryptophan side-chain mobilities in the 26-residue, cytolytic peptide melittin (MLT) were investigated by ¹⁵N and ¹³C NMR. Specifically, inverse-detected ¹⁵N T₁ and steady-state NOE measurements were made at 30 and 51 MHz on MLT at 22 °C enriched with ¹⁵N at six amide positions and in the Trp¹⁹ side chain. Both the disordered MLT monomer (1.2 mM peptide at pH 3.6 in neat water) and -helical MLT tetramer (4.0 mM peptide at pH 5.2 in 150 mM phosphate buffer) were examined. The relaxation data were analyzed in terms of the Lipari and Szabo model-free formalism with three parameters: _m, the correlation time for the overall rotation; S², a site-specific order parameter which is a measure of the amplitude of the internal motion; and _e, a local, effective correlation time of the internal motion. A comparison was made of motional parameters from the ¹⁵N measurements and from ¹³C measurements on MLT, the latter having been made here and previously [Kemple et al. (1997) Biochemistry, 36, 1678–1688]. _m and _e values were consistent from data on the two nuclei. In the MLT monomer, S² values for the backbone N-H and C-H vectors in the same residue were similar in value but in the tetramer the N-H order parameters were about 0.2 units larger than the C-H order parameters. The Trp side-chain N-H and C-H order parameters, and _e values were generally similar in both the monomer and tetramer. Implications of these results regarding the dynamics of MLT are examined.     

Intra-population variation in anemia status and its relationship to economic status and self-perceived health in the Mexican Family Life Survey: Implications for bioarchaeology

Recently scholars have advocated for the use of a critical biocultural approach in bioarchaeology, where osteological and dental markers of stress are used to understand the broader biosocial context of past populations. However, the ability to accomplish this task rests on the assumption that ultimate-level environmental stressors and well-being in the past can be reconstructed from the prevalence of pathologies in skeletal collections. Here we test this assumption using anemia prevalence in the Mexican Family Life Survey. Specifically we test three hypotheses: (1) that individuals sharing the same household are more likely to share anemia status; (2) anemia status is a predictor of economic status (a common proxy for broader environmental context); and (3) anemia status is related to self-rated health. Results demonstrate that: anemia status was not commonly shared between household members; there was a significant overlap in economic status between anemic and nonanemic individuals (i.e., anemia poorly predicted economic status) and; while anemia status was associated with self-perceived health, the majority of those who reported poor health were nonanemic while a significant number of those who reported very good health were anemic. We argue that these findings are likely related to variation in individual frailty, which is shaped by biological and cultural risk factors. Therefore, we advocate for greater incorporation of individual frailty into bioarchaeological investigations, and, in effort to overcome some of the difficulties associated with this task, increased use of data from living populations and greater collaboration between bioarchaeologists and human biologists. Am J Phys Anthropol 155:210–220, 2014. © 2014 Wiley Periodicals, Inc.     

A modified version of the digestion–ligation cloning method for more efficient molecular cloning

Here we describe a modified version of the digestion–ligation approach for efficient molecular cloning. In comparison with the original method, the modified method has the additional steps of gel purification and a second ligation after the first ligation of the linearized vector and DNA insert. During this process, the efficiency and reproducibility could be significantly improved for both stick-end cloning and blunt-end cloning. As an improvement of the very important molecular cloning technique, this method may find a wide range of applications in bioscience and biotechnology.     

Cytochrome c1 exhibits two binding sites for cytochrome c in plants

In plants, channeling of cytochrome c molecules between complexes III and IV has been purported to shuttle electrons within the supercomplexes instead of carrying electrons by random diffusion across the intermembrane bulk phase. However, the mode plant cytochrome c behaves inside a supercomplex such as the respirasome, formed by complexes I, III and IV, remains obscure from a structural point of view. Here, we report ab-initio Brownian dynamics calculations and nuclear magnetic resonance-driven docking computations showing two binding sites for plant cytochrome c at the head soluble domain of plant cytochrome c₁, namely a non-productive (or distal) site with a long heme-to-heme distance and a functional (or proximal) site with the two heme groups close enough as to allow electron transfer. As inferred from isothermal titration calorimetry experiments, the two binding sites exhibit different equilibrium dissociation constants, for both reduced and oxidized species, that are all within the micromolar range, thus revealing the transient nature of such a respiratory complex. Although the docking of cytochrome c at the distal site occurs at the interface between cytochrome c₁ and the Rieske subunit, it is fully compatible with the complex III structure. In our model, the extra distal site in complex III could indeed facilitate the functional cytochrome c channeling towards complex IV by building a “floating boat bridge” of cytochrome c molecules (between complexes III and IV) in plant respirasome.     

Alleviating social avoidance: Effects of single dose testosterone administration on approach–avoidance action

Testosterone is an important regulator of social–motivational behavior and is known for its dominance-enhancing and social-anxiolytic properties. However, to date no studies have systematically investigated the causal effect of testosterone on actual social approach–avoidance behavior in humans. The present study sets out to test the effects of testosterone administration in healthy female volunteers using an objective implicit measure of social motivational behavior: the social Approach–Avoidance Task, a reaction time task requiring participants to approach or avoid visually presented emotional (happy, angry, and neutral) faces. Participants showed significantly diminished avoidance tendencies to angry faces after testosterone administration. Testosterone did not affect approach–avoidance tendencies to social affiliation (happy) faces. Thus, a single dose testosterone administration reduces automatic avoidance of social threat and promotes relative increase of threat approach tendencies in healthy females. These findings further the understanding of the neuroendocrine regulation of social motivational behavior and may have direct treatment implications for social anxiety, characterized by persistent social avoidance.     

Proteomic analysis to identify early molecular targets of pregabalin in C6 glial cells

Pregabalin is a lipophilic amino acid derivative of γ‐amino butyric acid that displays anticonvulsant and analgesic activities against neuropathic pain. Although a role for glial cells as an important player in pain control and also as a new target for pain medicine has been suggested, the effect of pregabalin on glial cells has not been elucidated. In the present study, we have investigated the action of pregabalin on the glial cell proteome. To identify immediate early protein targets of pregabalin in glial cells, a differential proteomics approach in C6 rat glioma cells treated with pregabalin was used. Seven proteins that sensitively reacted to pregabalin treatment were identified using two‐dimensional gel electrophoresis and MALDI–TOF‐MS (matrix‐assisted laser‐desorption ionization–time‐of‐flight MS). The calcium‐ion‐binding chaperone, calreticulin, and the oxidative response protein, DJ‐1, were up‐regulated after pregabalin treatment. Hsp (heat‐shock protein)‐90‐β, cytoskeleton protein actin and myosin also showed quantitative expression profile differences. Functionally relevant to the proteome result, immediate actin depolymerization was observed after treatment with pregabalin. These results suggest a previously undefined role of pregabalin in the regulation of chaperone activity and cytoskeleton remodelling in glial cells.     

Postnatal handling reverses social anxiety in serotonin receptor 1A knockout mice

Mice lacking the serotonin receptor 1A (Htr1a knockout, Htr1a ^KO ) show increased innate and conditioned anxiety. This phenotype depends on functional receptor activity during the third through fifth weeks of life and thus appears to be the result of long-term changes in brain function as a consequence of an early deficit in serotonin signaling. To evaluate whether this phenotype can be influenced by early environmental factors, we subjected Htr1a knockout mice to postnatal handling, a procedure known to reduce anxiety-like behavior and stress responses in adulthood. Offspring of heterozygous Htr1a knockout mice were separated from their mother and exposed 15 min each day from postnatal day 1 (PD1) to PD14 to clean bedding. Control animals were left undisturbed. Maternal behavior was observed during the first 13 days of life. Adult male offspring were tested in the open field, social approach and resident–intruder tests and assessed for corticosterone response to restraint stress. Knockout mice showed increased anxiety in the open field and in the social approach test as well as an enhanced corticosterone response to stress. However, while no effect of postnatal handling was seen in wild-type mice, handling reduced anxiety-like behavior in the social interaction test and the corticosterone response to stress in knockout mice. These findings extend the anxiety phenotype of Htr1a ^KO mice to include social anxiety and demonstrate that this phenotype can be moderated by early environmental factors.