The hallmarks of cancer.

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

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Initial sequencing and analysis of the human genome.

The emergence of order in natural systems is a constant source of inspiration for both physical and biological sciences. While the spatial order characterizing for example the crystals has been the basis of many advances in contemporary physics, most complex systems in nature do not offer such high degree of order. Many of these systems form complex networks whose nodes are the elements of the system and edges represent the interactions between them. 
Traditionally complex networks have been described by the random graph theory founded in 1959 by Paul Erdohs and Alfred Renyi. One of the defining features of random graphs is that they are statistically homogeneous, and their degree distribution (characterizing the spread in the number of edges starting from a node) is a Poisson distribution. In contrast, recent empirical studies, including the work of our group, indicate that the topology of real networks is much richer than that of random graphs. In particular, the degree distribution of real networks is a power-law, indicating a heterogeneous topology in which the majority of the nodes have a small degree, but there is a significant fraction of highly connected nodes that play an important role in the connectivity of the network. 
The scale-free topology of real networks has very important consequences on their functioning. For example, we have discovered that scale-free networks are extremely resilient to the random disruption of their nodes. On the other hand, the selective removal of the nodes with highest degree induces a rapid breakdown of the network to isolated subparts that cannot communicate with each other. 
The non-trivial scaling of the degree distribution of real networks is also an indication of their assembly and evolution. Indeed, our modeling studies have shown us that there are general principles governing the evolution of networks. Most networks start from a small seed and grow by the addition of new nodes which attach to the nodes already in the system. This process obeys preferential attachment: the new nodes are more likely to connect to nodes with already high degree. We have proposed a simple model based on these two principles wich was able to reproduce the power-law degree distribution of real networks. Perhaps even more importantly, this model paved the way to a new paradigm of network modeling, trying to capture the evolution of networks, not just their static topology.

/pdf/statistical-mechanics-of-complex-networks-1zfjpvxipu.pdf

Statistical mechanics of complex networks

A genetic model for colorectal tumorigenesis

http://www.maths.qmul.ac.uk/%7Elatora/report_06.pdf

Complex networks: Structure and dynamics

The present invention relates to novel chimeric transactivating proteins comprising a functional portion of a DNA binding protein and a functional portion of a transcriptional activator protein. The chimeric transactivating proteins of the invention offer a variety of advantages, including the specific activation of expression of genes engineered to comprise transactivator responsive elements, thereby achieving exceptionally high levels of gene expression. Furthermore, in various embodiments of the invention, the transactivator proteins may be used to increase expression of some genes while repressing the expression of others, thus permitting a greater degree of control of gene expression patterns than other currently available systems. In preferred embodiments of the invention, the function of the chimeric lac repressor-HSVVP16 tansactivator proteins may be induced, for example, by chemical agents such as IPTG or changes in temperature. In a preferred specific embodiment of the invention, the ability to switch transactivator function on and off may be utilized in the context of transgenic animals and to develop cell lines capable of differentiation.

A Lac REPRESSOR-HSV VP16 CHIMERIC TRANSCRIPTIONAL ACTIVATOR PROTEIN SYSTEM FUNCTIONING IN TRANSFECTED MAMMALIAN CELLS

Transgenic mice harboring the SV40 large T antigen gene in a C57B1/6J genetic background (SV11) first express this gene at 1-2 weeks of age, develop papillomas of the choroid plexus by 80-90 days, and die within 125 days after birth. Transgenic mice harboring the same transgene in a (SV11-C57Bl/6J x NZW/lacJ) F1 genetic background express considerably lower levels of the transgene mRNA at comparable times after birth. As a consequence, tumor development and death are delayed. The NZW mice appear to contribute a dominant negative regulator for the expression of the SV40 large T antigen transgene, which in turn has a dramatic effect upon the time of appearance of tumors and the death of these transgenic animals.

Impact of the genetic background of transgenic mice upon the formation and timing of choroid plexus papillomas.

The purpose of this review is to bring together a large number of observations and facts that have been assembled during the study of the large tumor antigen protein (T antigen) encoded by simian virus 40 (SV40). This protein and its functions have been one the most intensively studied gene systems derived from a eukaryotic environment.

The SV40 Large Tumor Antigen

Phylogenetic trees based on mtDNA polymorphisms are often used to infer the history of recent human migrations. However, there is no consensus on which method to use. Most methods make strong assumptions which may bias the choice of polymorphisms and result in computational complexity which limits the analysis to a few samples/polymorphisms. For example, parsimony minimizes the number of mutations, which biases the results to minimizing homoplasy events. Such biases may miss the global structure of the polymorphisms altogether, with the risk of identifying a “common” polymorphism as ancient without an internal check on whether it either is homoplasic or is identified as ancient because of sampling bias (from oversampling the population with the polymorphism). A signature of this problem is that different methods applied to the same data or the same method applied to different datasets results in different tree topologies. When the results of such analyses are combined, the consensus trees have a low internal branch consensus. We determine human mtDNA phylogeny from 1737 complete sequences using a new, direct method based on principal component analysis (PCA) and unsupervised consensus ensemble clustering. PCA identifies polymorphisms representing robust variations in the data and consensus ensemble clustering creates stable haplogroup clusters. The tree is obtained from the bifurcating network obtained when the data are split into k = 2,3,4,…,k
 max clusters, with equal sampling from each haplogroup. Our method assumes only that the data can be clustered into groups based on mutations, is fast, is stable to sample perturbation, uses all significant polymorphisms in the data, works for arbitrary sample sizes, and avoids sample choice and haplogroup size bias. The internal branches of our tree have a 90% consensus accuracy. In conclusion, our tree recreates the standard phylogeny of the N, M, L0/L1, L2, and L3 clades, confirming the African origin of modern humans and showing that the M and N clades arose in almost coincident migrations. However, the N clade haplogroups split along an East-West geographic divide, with a “European R clade” containing the haplogroups H, V, H/V, J, T, and U and a “Eurasian N subclade” including haplogroups B, R5, F, A, N9, I, W, and X. The haplogroup pairs (N9a, N9b) and (M7a, M7b) within N and M are placed in nonnearest locations in agreement with their expected large TMRCA from studies of their migrations into Japan. For comparison, we also construct consensus maximum likelihood, parsimony, neighbor joining, and UPGMA-based trees using the same polymorphisms and show that these methods give consistent results only for the clade tree. For recent branches, the consensus accuracy for these methods is in the range of 1–20%. From a comparison of our haplogroups to two chimp and one bonobo sequences, and assuming a chimp-human coalescent time of 5 million years before present, we find a human mtDNA TMRCA of 206,000 ± 14,000 years before present.

/pdf/pca-and-clustering-reveal-alternate-mtdna-phylogeny-of-n-and-43auqnoj6k.pdf

PCA and clustering reveal alternate mtDNA phylogeny of N and M clades.

The present invention relates to novel chimeric transactivating proteins comprising a functional portion of a DNA binding protein and a functional portion of a transcriptional activator protein. The chimeric transactivating proteins of the invention offer a variety of advantages, including the specific activation of expression of genes engineered to comprise transactivator responsive elements, thereby achieving exceptionally high levels of gene expression. Furthermore, in various embodiments of the invention, the transactivator proteins may be used to increase expression of some genes while repressing the expression of others, thus permitting a greater degree of control of gene expression patterns than other currently available systems. In preferred embodiments of the invention, the function of the chimeric transactivator proteins may be induced, for example, by chemical agents (e.g. IPTG) or changes in temperature. In a preferred specific embodiment of the invention, the ability to switch transactivator function on and off may be utilized in the context of transgenic animals and to develop cell lines capable of differentiation.

Arnold J. Levine

Papers

A Lac REPRESSOR-HSV VP16 CHIMERIC TRANSCRIPTIONAL ACTIVATOR PROTEIN SYSTEM FUNCTIONING IN TRANSFECTED MAMMALIAN CELLS

Impact of the genetic background of transgenic mice upon the formation and timing of choroid plexus papillomas.

The SV40 Large Tumor Antigen

PCA and clustering reveal alternate mtDNA phylogeny of N and M clades.

Eukaryotic cells comprising a DNA sequence encoding a bacterial-viral chimeric transactivator protein