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CENP-meta, an essential kinetochore kinesin required for the maintenance of metaphase chromosome alignment in Drosophila.
CENP-meta has been identified as an essential, kinesin-like motor protein in Drosophila. The 257-kD CENP-meta protein is most similar to the vertebrate kinetochore-associated kinesin-like protein CENP-E, and like CENP-E, is shown to be a component of centromeric/kinetochore regions of Drosophila chromosomes. However, unlike CENP-E, which leaves the centromere/kinetochore region at the end of anaphase A, the CENP-meta protein remains associated with the centromeric/kinetochore region of the chromosome during all stages of the Drosophila cell cycle. P-element-mediated disruption of the CENP-meta gene leads to late larval/pupal stage lethality with incomplete chromosome alignment at metaphase. Complete removal of CENP-meta from the female germline leads to lethality in early embryos resulting from defects in metaphase chromosome alignment. Real-time imaging of these mutants with GFP-labeled chromosomes demonstrates that CENP-meta is required for the maintenance of chromosomes at the metaphase plate, demonstrating that the functions required to establish and maintain chromosome congression have distinguishable requirements
evolution, structure and function of metazoan splicing factor PRPF39
In the yeast U1 snRNP the Prp39/Prp42 heterodimer is essential for early steps of spliceosome assembly. In metazoans no Prp42 ortholog exists, raising the question how the heterodimer is functionally substituted. Here we present the crystal structure of murine PRPF39, which forms a homodimer. Structure-guided point mutations disrupt dimer formation and inhibit splicing, manifesting the homodimer as functional unit. PRPF39 expression is controlled by NMD-inducing alternative splicing in mice and human, suggesting a role in adapting splicing efficiency to cell type specific requirements. A phylogenetic analysis reveals coevolution of shortened U1 snRNA and the absence of Prp42, which correlates with overall splicing complexity in different fungi. While current models correlate the diversity of spliceosomal proteins with splicing complexity, our study highlights a contrary case. We find that organisms with higher splicing complexity have substituted the Prp39/Prp42 heterodimer with a PRPF39 homodimer
The Jones polynomial and graphs on surfaces
The Jones polynomial of an alternating link is a certain specialization of
the Tutte polynomial of the (planar) checkerboard graph associated to an
alternating projection of the link. The Bollobas-Riordan-Tutte polynomial
generalizes the Tutte polynomial of planar graphs to graphs that are embedded
in closed oriented surfaces of higher genus.
In this paper we show that the Jones polynomial of any link can be obtained
from the Bollobas-Riordan-Tutte polynomial of a certain oriented ribbon graph
associated to a link projection. We give some applications of this approach.Comment: 19 pages, 9 figures, minor change
Flexible RNA design under structure and sequence constraints using formal languages
The problem of RNA secondary structure design (also called inverse folding)
is the following: given a target secondary structure, one aims to create a
sequence that folds into, or is compatible with, a given structure. In several
practical applications in biology, additional constraints must be taken into
account, such as the presence/absence of regulatory motifs, either at a
specific location or anywhere in the sequence. In this study, we investigate
the design of RNA sequences from their targeted secondary structure, given
these additional sequence constraints. To this purpose, we develop a general
framework based on concepts of language theory, namely context-free grammars
and finite automata. We efficiently combine a comprehensive set of constraints
into a unifying context-free grammar of moderate size. From there, we use
generic generic algorithms to perform a (weighted) random generation, or an
exhaustive enumeration, of candidate sequences. The resulting method, whose
complexity scales linearly with the length of the RNA, was implemented as a
standalone program. The resulting software was embedded into a publicly
available dedicated web server. The applicability demonstrated of the method on
a concrete case study dedicated to Exon Splicing Enhancers, in which our
approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational
Biology and Biomedical Informatics (2013
Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures
Large RNA molecules often carry multiple functional domains whose spatial
arrangement is an important determinant of their function. Pre-mRNA splicing,
furthermore, relies on the spatial proximity of the splice junctions that can
be separated by very long introns. Similar effects appear in the processing of
RNA virus genomes. Albeit a crude measure, the distribution of spatial
distances in thermodynamic equilibrium therefore provides useful information on
the overall shape of the molecule can provide insights into the interplay of
its functional domains. Spatial distance can be approximated by the
graph-distance in RNA secondary structure. We show here that the equilibrium
distribution of graph-distances between arbitrary nucleotides can be computed
in polynomial time by means of dynamic programming. A naive implementation
would yield recursions with a very high time complexity of O(n^11). Although we
were able to reduce this to O(n^6) for many practical applications a further
reduction seems difficult. We conclude, therefore, that sampling approaches,
which are much easier to implement, are also theoretically favorable for most
real-life applications, in particular since these primarily concern long-range
interactions in very large RNA molecules.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Image Forgery Localization Based on Multi-Scale Convolutional Neural Networks
In this paper, we propose to utilize Convolutional Neural Networks (CNNs) and
the segmentation-based multi-scale analysis to locate tampered areas in digital
images. First, to deal with color input sliding windows of different scales, a
unified CNN architecture is designed. Then, we elaborately design the training
procedures of CNNs on sampled training patches. With a set of robust
multi-scale tampering detectors based on CNNs, complementary tampering
possibility maps can be generated. Last but not least, a segmentation-based
method is proposed to fuse the maps and generate the final decision map. By
exploiting the benefits of both the small-scale and large-scale analyses, the
segmentation-based multi-scale analysis can lead to a performance leap in
forgery localization of CNNs. Numerous experiments are conducted to demonstrate
the effectiveness and efficiency of our method.Comment: 7 pages, 6 figure
FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome.
Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for estimating exon-inclusion ratios at the genome scale all require the existence of a reference transcriptome. In this paper, we propose an alignment-free method, FreePSI, to perform genome-wide estimation of exon-inclusion ratios from RNA-Seq data without relying on the guidance of a reference transcriptome. It uses a novel probabilistic generative model based on k-mer profiles to quantify the exon-inclusion ratios at the genome scale and an efficient expectation-maximization algorithm based on a divide-and-conquer strategy and ultrafast conjugate gradient projection descent method to solve the model. We compare FreePSI with the existing methods on simulated and real RNA-seq data in terms of both accuracy and efficiency and show that it is able to achieve very good performance even though a reference transcriptome is not provided. Our results suggest that FreePSI may have important applications in performing alternative splicing analysis for organisms that do not have quality reference transcriptomes. FreePSI is implemented in C++ and freely available to the public on GitHub
Recasting Residual-based Local Descriptors as Convolutional Neural Networks: an Application to Image Forgery Detection
Local descriptors based on the image noise residual have proven extremely
effective for a number of forensic applications, like forgery detection and
localization. Nonetheless, motivated by promising results in computer vision,
the focus of the research community is now shifting on deep learning. In this
paper we show that a class of residual-based descriptors can be actually
regarded as a simple constrained convolutional neural network (CNN). Then, by
relaxing the constraints, and fine-tuning the net on a relatively small
training set, we obtain a significant performance improvement with respect to
the conventional detector
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