POU domain genes and the immunoglobulin octamer motif in chickens

This research was undertaken to test the hypothesis that multiple POU genes exist and that POU proteins are involved in transcriptional regulation in the chicken. The POU protein Oct-2 has been hypothesized to partially regulate immunoglobulin gene expression through its interaction with the octamer motif found in the promoter of immunoglobulin genes. Transcriptional regulation of immunoglobulin genes provides a model for tissue-specific gene expression in the immune system. In searching for a chicken Oct-2 homologue, two partial chicken POU domain genes were identified. A cDNA clone encoding the POU domain of Brn-3a was isolated and showed near identity to the human Brn-3a sequence (100% at the a.a. level). Chicken Brn-3a was mapped to linkage group E48 in the East Lansing chicken genome mapping reference population. A Skn-1/Epoc-1/Oct-11 genomic clone was identified and mapped to chicken linkage group E49, to an area of synteny with human chromosome 11q23 and mouse chromosome 9. Octamer-binding protein expression patterns in multiple chicken tissues demonstrated that octamer-binding protein complexes existed in ovary, cerebrum, liver, lung, kidney, spleen, thymus, bursa, MSB1 (T cell line), and DT40 (B cell line). Every tissue had at least two octamer-binding proteins, with a total of seven unique chicken protein complexes. A comparison between mouse and chicken octamer-binding proteins identified a unique chicken octamer-binding protein, slightly faster migrating than mouse Oct-2. Chicken Oct-1 was expressed in all tissues except liver. The chicken immunoglobulin lambda light chain promoter contains an octamer motif (-106) and a TATA box (-70). Chicken B and T lymphocyte cell lines were used to determine activity of both the promoter and the octamer motif. The promoter was functional only in the B cell line and required an enhancer sequence. Mutation of the octamer motif abolished the transcriptional activity of the immunoglobulin promoter. These results suggest that the chicken immunoglobulin promoter functions similarly to its mammalian counter parts, in that the chicken immunoglobulin lambda light chain promoter plays a role in tissue-specificity and requires an enhancer and an intact octamer motif

Social and Academic Advantages and Disadvantages of Within-class Heterogeneous and Homogeneous Ability Grouping

This study reviews research and examines studies on the effects of within-class ability grouping on middle school student\u27s academic achievement and motivation to learn. Four seventh grade science classes were placed into 16 randomized and then heterogeneous and homogenous ability groups and tested after each. The main findings indicate that high ability students may succeed in either ability grouping style. Average ability students showed better group performance in homogenous ability groups but tested better as a result of heterogeneous grouping. Low ability students experienced much greater academic achievement as a result of heterogeneous ability groups. Finally, topics for future areas of research are discussed

B-1a cells acquire their unique characteristics by bypassing the pre-BCR selection stage

B-1a cells are long-lived, self-renewing innate-like B cells that predominantly inhabit the peritoneal and pleural cavities. In contrast to conventional B-2 cells, B-1a cells have a receptor repertoire that is biased towards bacterial and self-antigens, promoting a rapid response to infection and clearing of apoptotic cells. Although B-1a cells are known to primarily originate from fetal tissues, the mechanisms by which they arise has been a topic of debate for many years. Here we show that in the fetal liver versus bone marrow environment, reduced IL-7R/STAT5 levels promote immunoglobulin kappa gene recombination at the early pro-B cell stage. As a result, differentiating B cells can directly generate a mature B cell receptor (BCR) and bypass the requirement for a pre-BCR and pairing with surrogate light chain. This 'alternate pathway' of development enables the production of B cells with self-reactive, skewed specificity receptors that are peculiar to the B-1a compartment. Together our findings connect seemingly opposing lineage and selection models of B-1a cell development and explain how these cells acquire their unique properties

Wide-range continuous tuning of the thermal conductivity of La0.5Sr0.5CoO3−δ\rm La_{0.5}Sr_{0.5}CoO_{3-\delta} films via room-temperature ion-gel gating

Solid-state control of the thermal conductivity of materials is of exceptional interest for novel devices such as thermal diodes and switches. Here, we demonstrate the ability to continuously tune the thermal conductivity of nanoscale films of $\rm La_{0.5}Sr_{0.5}CoO_{3-\delta}$ (LSCO) by a factor of over 5, via a room-temperature electrolyte-gate-induced non-volatile topotactic phase transformation from perovskite (with $\delta \approx 0.1$) to an oxygen-vacancy-ordered brownmillerite phase (with $\delta=0.5$), accompanied by a metal-insulator transition. Combining time-domain thermoreflectance and electronic transport measurements, model analyses based on molecular dynamics and Boltzmann transport, and structural characterization by X-ray diffraction, we uncover and deconvolve the effects of these transitions on heat carriers, including electrons and lattice vibrations. The wide-range continuous tunability of LSCO thermal conductivity enabled by low-voltage (below 4 V) room-temperature electrolyte gating opens the door to non-volatile dynamic control of thermal transport in perovskite-based functional materials, for thermal regulation and management in device applications

Germinal center reutilization by newly activated B cells

Germinal centers (GCs) are specialized structures in which B lymphocytes undergo clonal expansion, class switch recombination, somatic hypermutation, and affinity maturation. Although these structures were previously thought to contain a limited number of isolated B cell clones, recent in vivo imaging studies revealed that they are in fact dynamic and appear to be open to their environment. We demonstrate that B cells can colonize heterologous GCs. Invasion of primary GCs after subsequent immunization is most efficient when T cell help is shared by the two immune responses; however, it also occurs when the immune responses are entirely unrelated. We conclude that GCs are dynamic anatomical structures that can be reutilized by newly activated B cells during immune responses

Network-based functional enrichment

<p>Abstract</p> <p>Background</p> <p>Many methods have been developed to infer and reason about molecular interaction networks. These approaches often yield networks with hundreds or thousands of nodes and up to an order of magnitude more edges. It is often desirable to summarize the biological information in such networks. A very common approach is to use gene function enrichment analysis for this task. A major drawback of this method is that it ignores information about the edges in the network being analyzed, i.e., it treats the network simply as a set of genes. In this paper, we introduce a novel method for functional enrichment that explicitly takes network interactions into account.</p> <p>Results</p> <p>Our approach naturally generalizes Fisher’s exact test, a gene set-based technique. Given a function of interest, we compute the subgraph of the network induced by genes annotated to this function. We use the sequence of sizes of the connected components of this sub-network to estimate its connectivity. We estimate the statistical significance of the connectivity empirically by a permutation test. We present three applications of our method: i) determine which functions are enriched in a given network, ii) given a network and an interesting sub-network of genes within that network, determine which functions are enriched in the sub-network, and iii) given two networks, determine the functions for which the connectivity improves when we merge the second network into the first. Through these applications, we show that our approach is a natural alternative to network clustering algorithms.</p> <p>Conclusions</p> <p>We presented a novel approach to functional enrichment that takes into account the pairwise relationships among genes annotated by a particular function. Each of the three applications discovers highly relevant functions. We used our methods to study biological data from three different organisms. Our results demonstrate the wide applicability of our methods. Our algorithms are implemented in C++ and are freely available under the GNU General Public License at our supplementary website. Additionally, all our input data and results are available at <url>http://bioinformatics.cs.vt.edu/~murali/supplements/2011-incob-nbe/</url>.</p