Role of hydrophobic interaction in hapten-antibody binding

The precipitation reaction of bovine serum albumin coupled with p-azophenylleucine with homologous antibody was inhibited by several structurally related haptens. The isobutyl group substituent on alpha-carbon atom of the leucine residue contributed more than -5.8 Kcal/mol to the free energy of binding. This value was consistent with the free energy change expected from the transfer of n-butane from an aqueous environment to liquid n-butane. The observed contribution was explained, in terms of the hydrophobic interaction of the isobutyl group with the antigen binding site of the antibody molecule. These results were also compared with other hapten-antibody systems.</p

Think Globally, Embed Locally - Locally Linear Meta-embedding of Words

Distributed word embeddings have shown superior performances in numerous Natural Language Processing (NLP) tasks. However, their performances vary significantly across different tasks, implying that the word embeddings learnt by those methods capture complementary aspects of lexical semantics. Therefore, we believe that it is important to combine the existing word embeddings to produce more accurate and complete \emph{meta-embeddings} of words. For this purpose, we propose an unsupervised locally linear meta-embedding learning method that takes pre-trained word embeddings as the input, and produces more accurate meta embeddings. Unlike previously proposed meta-embedding learning methods that learn a global projection over all words in a vocabulary, our proposed method is sensitive to the differences in local neighbourhoods of the individual source word embeddings. Moreover, we show that vector concatenation, a previously proposed highly competitive baseline approach for integrating word embeddings, can be derived as a special case of the proposed method. Experimental results on semantic similarity, word analogy, relation classification, and short-text classification tasks show that our meta-embeddings to significantly outperform prior methods in several benchmark datasets, establishing a new state of the art for meta-embeddings

Changes in saccadic eye movement and smooth pursuit gain in patients with acquired comitant esotropia after strabismus surgery

This study investigates the change in horizontal saccadic eye movement and smooth pursuit in patients with acquired comitant esotropia (ACE), before and after strabismus surgery. The horizontal saccades and pursuit in 11 patients with ACE were recorded using a video eye-tracker under binocular viewing before and after strabismus surgery. Participants were instructed to fixate on the new target as rapidly as possible when it randomly appeared at either 18.3° rightward or 18.3° leftward. For smooth pursuit, participants were asked to track, as accurately as possible, a step-ramp target moving at ±6.1°/s. The asymmetry of adduction-abduction and the binocular coordination in gains of saccade and pursuit were compared between the pre- and post-surgical data. The asymmetry of adduction-abduction saccade gain in each eye after surgery tended to be smaller than that before surgery. The binocular coordination of saccade showed significant improvement after surgery in only the non-dominant eye direction. Adduction-abduction asymmetry in the smooth pursuit gain in each eye after surgery tended to be smaller than before surgery. After surgery, the binocular coordination of pursuit was improved significantly in both directions. In patients with ACE, binocular coordination of saccade and smooth pursuit was poor. Binocular coordination of saccade and pursuit seems to be improved due to the improvement in ocular deviation angle and binocular visual function after surgery

A chemical biology approach reveals an opposite action between thermospermine and auxin in xylem development in Arabidopsis thaliana

Thermospermine, a structural isomer of spermine, is produced through the action of ACAULIS5 (ACL5) and suppresses xylem differentiation in Arabidopsis thaliana. To elucidate the molecular basis of the function of thermospermine, we screened chemical libraries for compounds that can modulate xylem differentiation in the acl5 mutant, which is deficient in thermospermine and shows a severe dwarf phenotype associated with excessive proliferation of xylem vessels. We found that the isooctyl ester of a synthetic auxin, 2,4-D, remarkably enhanced xylem vessel differentiation in acl5 seedlings. 2,4-D, 2,4-D analogs and IAA analogs, including 4-chloro IAA (4-Cl-IAA) and IAA ethyl ester, also enhanced xylem vessel formation, while IAA alone had little or no obvious effect on xylem differentiation. These effects of auxin analogs were observed only in the acl5 mutant but not in the wild type, and were suppressed by the anti-auxin, p-chlorophenoxyisobutyric acid (PCIB) and alpha-(phenyl ethyl-2-one)-IAA (PEO-IAA), and also by thermospermine. Furthermore, the suppressor of acaulis51-d (sac51-d) mutation, which causes SAC51 overexpression in the absence of thermospermine and suppresses the dwarf phenotype of acl5, also suppressed the effect of auxin analogs in acl5. These results suggest that the auxin signaling that promotes xylem differentiation is normally limited by SAC51-mediated thermospermine signaling but can be continually stimulated by exogenous auxin analogs in the absence of thermospermine. The opposite action between thermospermine and auxin may fine-tune the timing and spatial pattern of xylem differentiation

Differential genome-wide gene expression profiling of bovine largest and second-largest follicles: identification of genes associated with growth of dominant follicles

<p>Abstract</p> <p>Background</p> <p>Bovine follicular development is regulated by numerous molecular mechanisms and biological pathways. In this study, we tried to identify differentially expressed genes between largest (F1) and second-largest follicles (F2), and classify them by global gene expression profiling using a combination of microarray and quantitative real-time PCR (QPCR) analysis. The follicular status of F1 and F2 were further evaluated in terms of healthy and atretic conditions by investigating mRNA localization of identified genes.</p> <p>Methods</p> <p>Global gene expression profiles of F1 (10.7 +/- 0.7 mm) and F2 (7.8 +/- 0.2 mm) were analyzed by hierarchical cluster analysis and expression profiles of 16 representative genes were confirmed by QPCR analysis. In addition, localization of six identified transcripts was investigated in healthy and atretic follicles using in situ hybridization. The healthy or atretic condition of examined follicles was classified by progesterone and estradiol concentrations in follicular fluid.</p> <p>Results</p> <p>Hierarchical cluster analysis of microarray data classified the follicles into two clusters. Cluster A was composed of only F2 and was characterized by high expression of 31 genes including IGFBP5, whereas cluster B contained only F1 and predominantly expressed 45 genes including CYP19 and FSHR. QPCR analysis confirmed AMH, CYP19, FSHR, GPX3, PlGF, PLA2G1B, SCD and TRB2 were greater in F1 than F2, while CCL2, GADD45A, IGFBP5, PLAUR, SELP, SPP1, TIMP1 and TSP2 were greater in F2 than in F1. In situ hybridization showed that AMH and CYP19 were detected in granulosa cells (GC) of healthy as well as atretic follicles. PlGF was localized in GC and in the theca layer (TL) of healthy follicles. IGFBP5 was detected in both GC and TL of atretic follicles. GADD45A and TSP2 were localized in both GC and TL of atretic follicles, whereas healthy follicles expressed them only in GC.</p> <p>Conclusion</p> <p>We demonstrated that global gene expression profiling of F1 and F2 clearly reflected a difference in their follicular status. Expression of stage-specific genes in follicles may be closely associated with their growth or atresia. Several genes identified in this study will provide intriguing candidates for the determination of follicular growth.</p