The investigation of the interplay between genes, proteins, metabolites and diseases plays a central role in molecular and cellular biology. Whole genome sequencing has made it possible to examine the behavior of all the genes in a genome by high-throughput experimental techniques and to pinpoint molecular interactions on a genome-wide scale, which form the backbone of systems biology. In particular, Bayesian network (BN) is a powerful tool for the ab-initial identification of causal and non-causal relationships between biological factors directly from experimental data. However, scalability is a crucial issue when we try to apply BNs to infer such interactions. In this paper, we not only introduce the Bayesian network formalism and its applications in systems biology, but also review recent technical developments for scaling up or speeding up the structural learning of BNs, which is important for the discovery of causal knowledge from large-scale biological datasets. Specifically, we highlight the basic idea, relative pros and cons of each technique and discuss possible ways to combine different algorithms towards making BN learning more accurate and much faster.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is g-2 herpesvirus with latency and lytic replication stages in its life-cycle. The viral replication and transcription activator (RTA) is the key protein for triggering KSHV lytic gene expression and replication from latency. In this review, we will discuss the gene expression program in KSHV lytic replication and latency, the regulation of the RTA expression, the RTA protein and the mechanisms that RTA utilizes to transactivate its target genes. We will focus on the RTA-mediated transactivation mechanisms, including DNA-binding, interacting with cellular co-factors and promoting repressor degradation.

The lethal giant larvae (lgl) gene was first identified more than 30 years ago in Drosophila and characterized as a tumor suppressor gene. Studies in budding yeast, flies and mammals all indicate that the evolutionarily conserved Lgl family proteins play an important role in cell polarity. Sro7/77, the yeast Lgl homologues, are important for the establishment and reinforcement of cell polarity through their localized interaction and kinetic activation of the post-Golgi secretion machinery. As for higher eukaryotes, both in epithelial polarity and asymmetric cell division, the role of Lgl protein is deployed by localizing proteins to the membrane in a polarized fashion. In addition, Lgl is transiently required during the establishment phase of polarity, implicating that Lgl functions at strategic time points for proliferation control. Studies in cancer biology provide direct connections between malfunction of Lgl and formation, progression and metastasis of various cancers. Here, we review recent advances in the field, focusing on the function of the Lgl family in cellular polarization.

The neural modulation in central auditory system plays an important role in perception and processing of sound signal and auditory cognition. The inferior colliculus (IC) is both a relay station in central auditory pathway and a sub-cortical auditory center doing the sound signal processing. IC is also modulated by the descending projections from the cortex and auditory thalamus, medial geniculate body, and these neural modulations not only can affect ongoing sound signal processing but can also induce plastic changes in IC.

For survival, bats of the suborder Microchiropetra emit intense ultrasonic pulses and analyze the weak returning echoes to extract the direction, distance, velocity, size, and shape of the prey. Although these bats and other mammals share the common layout of the auditory pathway and sound coding mechanism, they have highly developed auditory systems to process biologically relevant pulses at the expense of a reduced visual system. During this active biosonar behavior, they progressively shorten the pulse duration, decrease the amplitude and pulse-echo gap as they search, approach and finally intercept the prey. Presumably, these changes in multiple pulse parameters throughout the entire course of hunting enable them to extract maximal information about localized prey from the returning echoes. To hunt successfully, the auditory system of these bats must be less sensitive to intense emitted pulses but highly sensitive to weak returning echoes. They also need to recognize and differentiate the echoes of their emitted pulses from echoes of pulses emitted by other conspecifics. Past studies have shown the following mechanical and neural adaptive mechanisms underlying the successful bat biosonar behavior: (1) Forward orienting and highly mobile pinnae for effective scanning, signal reception, sound pressure transformation and mobile auditory sensitivity; (2) Avoiding and detecting moving targets more successfully than stationary ones; (3) Coordinated activity of highly developed laryngeal and middle ear muscles during pulse emission and reception; (4) Mechanical and neural attenuation of intense emitted pulses to prepare for better reception of weak returning echoes; (5) Increasing pulse repetition rate to improve multiple-parametric selectivity to echoes; (6) Dynamic variation of duration selectivity and recovery cycle of auditory neurons with hunting phase for better echo analysis; (7) Maximal multiple-parametric selectivity to expected echoes returning within a time window after pulse emission; (8) Pulse-echo delay-sensitive neurons in higher auditory centers for echo ranging; (9) Corticofugal modulation to improve on-going multiple-parametric signal processing and reorganize signal representation, and (10) A large area of the superior colliculus, pontine nuclei and cerebellum that is sensitive to sound for sensori-motor integration. All these adaptive mechanisms facilitate the bat to effectively extract prey features for successful hunting.

Pollination is one of the most important steps during fertilization and sexual reproduction in plants, and numerous cell-cell interaction events occur between the pistil and the pollen grain/tube during this process. The pollen-stigma interaction is a highly selective process which leads to compatible or incompatible pollination. Previous studies in Solanaceae, Papaveraceae, and Brassicaceae provided some important insights into pollen-stigma recognition in self-incompatible systems. In recent years, considerable data have been available regarding pollen-stigma interaction during self-compatible pollination. In this review, we focus on discussing current knowledge on stigma factors that regulate pollen-stigma interaction in self-compatible systems in comparison with self-incompatible systems.

The recretohalophyte with specialized salt-secreting structures including salt glands and salt bladders can secrete salt from their bodies and easily adapt themselves to many kinds of salt habitats. Salt glands and salt bladders, arose from dermatogen cells, are excretory organs specially adapted for dealing with ionic homeostasis in the cells of recretohalophytes. The main function of salt glands or salt bladders is to secrete excess ions that invade the plant. The structures of salt glands or salt bladders differ among plant species. In addition to structural differences, salt glands also differ in their secretion abilities. In this review, we mainly focus on recent progress in the mechanism of salt excretion of salt glands and salt bladders, and in particular, emphasize the vesicle-mediated secretion systems from the vacuole to the plasmalemma and the possibly involved membrane-bound translocating proteins for salt secretion of plant gland secretory cell.

MicroRNAs are one class of small single-stranded RNA of about 22nt serving as important negative gene regulators. In animals, miRNAs mainly repress protein translation by binding itself to the 3’ UTR regions of mRNAs with imperfect complementary pairing. Although bioinformatics investigations have resulted in a number of target prediction tools, all of these have a common shortcoming—a high false positive rate. Therefore, it is important to further filter the predicted targets. In this paper, based on miRNA:target duplex, we construct a second-order Hidden Markov Model, implement Baum-Welch training algorithm and apply this model to further process predicted targets. The model trains the classifier by 244 positive and 49 negative miRNA:target interaction pairs and achieves a sensitivity of 72.54%, specificity of 55.10% and accuracy of 69.62% by 10-fold cross-validation experiments. In order to further verify the applicability of the algorithm, previously collected datasets, including 195 positive and 38 negative, are chosen to test it, with consistent results. We believe that our method will provide some guidance for experimental biologists, especially in choosing miRNA targets for validation.

A fundamental aspect of cancer development is cancer cell proliferation. Seeking for chemical agents that can interfere with cancer cell growth has been of great interest over the years. In our study, we found that a benzoxazine derivative, (6-tert-butyl-3,4-dihydro-2H-benzo[b][1,4]oxazin-3-yl) methanol (TBM), could inhibit cell growth and caused significant cell cycle arrest in pulmonary adenocarcinoma A549 and H460 cells with wild-type p53, while not affecting the cell cycle distribution in p53-deleted H1299 lung adenocarcinoma cells. Since P53 plays an important role in regulating cell cycle progression, we analyzed the protein level of p53 by Western blot, and detected a significant elevation of p53 level after TBM treatment in A549 and H460 cells. The data suggested that TBM might specifically inhibit the proliferation of p53 wild-type lung adenocarcinoma cells through a p53-dependent cell cycle control pathway. More interestingly, results indicated that TBM might serve as a useful tool for studying the molecular mechanisms of lung cancer cell growth and cell cycle control, especially for the biologic process regulated by P53.

The genus of Secale has many agronomically important characters. In order to use the best of this species, markers tracking the rye chromatin incorporated into wheat must be developed. In this study, one rye genome-specific random amplified polymorphic DNA (RAPD) marker was isolated from Secale africanum (R^a genome). Two cloned markers, named OPP13₁₁₆₅ and OPP13₆₆₂, were 1165 bp and 662 bp, respectively. Sequence analysis revealed that OPP13₁₁₆₅ was highly homologous to a part of a new class of transposon-like gene called the Revolver family, and OPP13₆₆₂ was partially similar to LTR gypsy-like retrotransposon. Fluorescence in situ hybridization (FISH) showed only OPP13₁₁₆₅ localized within the whole arms of rye except their terminal regions and no signal was detected on wheat chromosomes, while OPP13₆₆₂ had no hybridization signal detected on wheat and rye genomes. Based on these sequences, two pairs of sequence-characterized amplified region (SCAR) primers were designed, and the resulted SCAR markers were able to target both cultivated and wild Secale species. The FISH patterns and the two SCAR markers should be able to identify and track all wheat-rye translocation lines, especially the S. africanum chromatin.