Biomedical subjects

Juan Bai

Publications and source records attributed to Juan Bai.

6 recordsLinked to original sources

PubMed2025

Architectural transcription factors collectively shape nuclear radial positioning of chromatin contacts.

The measurement of three-dimensional genome folding in the nucleus, mostly through Hi-C methods, is expressed as contact frequencies between genomic segments, without anchoring to physical axes of the spherical nucleus. Here, we mapped the chromatin contacts along nuclear radial axis and built radial score by factoring in contact frequencies. The chromatin high-order structures exhibit rich diversity along radial axis. Furthermore, the proximal trans contacts retrieved by radial score reveal conserved active/inactive chromatin segregation across intra- and interchromosomal interactions. Ablation of CTCF proteins disrupts chromatin loops with mild changes to chromatin radial positioning. By acutely perturbing multiple transcription factor (TF) occupancy, chromatin loop dissolutions are often accompanied by radial dissociations between two anchors. Our work provides a genome architecture reference map adhering to nuclear physical axis and suggests that multiple architectural TFs collectively shape nuclear positioning of chromatin and their contacts, with contacts serving as forces on chromatin positioning as well.

Chromatin↗

PubMed2004

Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin.

The crystal structure of a potato calmodulin (PCM6) was solved by molecular replacement and refined to a crystallographic R factor of 22.8% (R(free) = 25.0%) using X-ray diffraction data in the resolution range 8.0-2.0 A. This is the first report of the three-dimensional structure of a plant Ca(2+)-calmodulin. PCM6 crystallizes in a crystal form that belongs to space group P2(1)2(1)2(1), which is different to that of most other calmodulin crystals. The main structural difference between PCM6 and the other calmodulins is in the central helix region and appears to be caused by crystal packing. The surface properties of PCM6 molecules were compared with those of animal calmodulins, which provided an explanation for the unique crystal-packing state of PCM6.

Amino Acid Sequence↗

PubMed2004

Line at shape-from-shadow border tested with stereo.

Kennedy and Bai (2000 Perception 29 399-408) argued incorrect border polarity blocked perception of faces in shape-from-shadow 'Mooney faces' with dark lines at the contour, a display inspired by Hering. Their hypothesis was tested with several displays, notably binocular gratings made of lines of dots. The stereo-induced depth involved a shadow falling on two surface planes. Most of a dark-dotted (shadow) region appeared to be on one surface, but a strip of dark dots at the shadow's border appeared to be on another-to the fore or rear. Control conditions involved 'negative' images (white dots). Subjects saw the shadowed object as easily in dark-dotted images with stereo depth as in an image with uniform depth for all the dots, and more readily than in the negatives. Our results favour the border-polarity hypothesis.

Adult↗

PubMed2004

[Fluorescence of Tb(3+) -calmodulin complex and its analytical application].

Calmodulin (CaM) is a ubiquitous Ca(2+) -binding protein of eukaryotes, and regulates a broad spectrum of fundamental cellular processes. CaM harbors four binding domains, among which domains I, II and III contain no tyrosine, only domain IV has one tyrosine for plant species. In contrast to mammals, plants express numerous CaM isoforms that exhibit differential activation or inhibition of CaM dependent enzymes in vitro. In the present study, the isoform II of Arabidopsis thaliana CaM was used to test the binding properties of metal ion to CaM by Tb3+ fluorescence. The increase in fluorescence was monitored at 545 nm as a function of the number of Tb3+ bound to CaM using direct (221 nm) and indirect (280 nm ) excitation. Upon direct excitation of Tb(3+) -CaM, the fluorescence of Tb3+ increased markedly, and one of the pathways of energy dissipation of the excited state of Tb3+ was energy transfer to the vibrational levels of water molecules in the hydration sphere around the Tb3+ ion. When waters of hydration were removed as a result of Tb3+ binding to CaM, an increase in rate constants of luminescence was observed. The titration curve with direct excitation increased up to 4 mol of Tb3+/mol of CaM before the onset of a plateau, in agreement with the expected maximum of four binding sites. Using indirect excitation at 280 nm, the resultant titration curve was sigmoid, albeit with less fluorescence intensity, also reached a maximum at a ratio of 4 mol of Tb3+/mol of CaM, in which the first phase exhibits an end at 2 : 1, and in this phase there was only a small increase in Tb3+ fluorescence. The fact that only the second pair of added Tb3+ shows a large enhancement in Tb3+ fluorescence suggests that it is Tb3+ bound to the low affinity sites that can accept energy from tyrosine group. The turning points of fluorescence titration curves were used to estimate the concentrations of CaM on the base of CTb3+ = 4c(CaM).

Binding Sites↗

PubMed2002

Haptic pictures: fit judgments predict identification, recognition memory, and confidence.

DAngiulli et al (1998 Scandinavian Journal of Psychology 39 187-190) found blind and sighted (blindfolded) children identified common objects in raised-outline drawings explored haptically, and corrected themselves without feedback. The self-correction suggests that participants can assess the extent to which the referents they suggest as possible identifications fit the haptic pictures. Indeed, when we asked subjects to identify haptic pictures, and to judge how well the referents they mentioned fitted the pictures, their fit judgments predicted the accuracy of their suggestions. Also, when one group of subjects offered the suggestions and another group assessed the fit of the suggestions to the pictures, the fit judgments predicted the accuracy of the suggestions. Further, good fit predicted successful recognition memory. In addition, both high and low fit judgments were made confidently, so the range of confidence judgments was smaller than the range of fit judgments. Finally, visual judgments of fit by one group predicted the level of success of the suggestions from another (haptic) group. In sum, subjects assess their suggested identifications appropriately, most likely on the basis of object shape criteria, outlined surface edges, and use of a vantage point.

Blindness↗

PubMed2001

Judgments of Frequency and Recency in a Distributed Memory Model.

TODAM is a theory of distributed associative memory based on the convolution-correlation formalism of A. Borsellino and T. Poggio (1973, Kybernetik, 122, 113-122), and TODAM2 is a revised version which includes context, auto-associations for binding, a dual basis for item information, and mediators for associative information. It can explain some complex interactions (differential forgetting and differential attention) between item and associative information. In this paper we derive the basic expressions for the memory-probe dot product for the 2x2 cases (item and pair study crossed with item and pair probe), and then we apply these expressions to judgments of frequency (JOF) and judgments of recency (JOR). We report an experiment which tests both JOF and JOR for single items with post-cuing to control for encoding strategies and suggest an attenuation factor for repetition to improve the fits. With attenuation, TODAM2 can fit the JOR data, but the JOF fits, while not too bad, consistently predict too much dependence between item and associative information. Copyright 2001 Academic Press.

Journal Article↗