The specificity of the transforming growth factor beta receptor kinases determined by a spatially addressable peptide library.

Type I and II receptors for the transforming growth factor beta (TGF-beta) are transmembrane serine/threonine kinases that are essential for TGF-beta signaling. However, little is known about their in vivo substrates or signal transduction pathways. To determine the substrate specificity of these kinases, we developed combinatorial peptide libraries synthesized on a hydrophilic matrix that is easily accessible to proteins in aqueous solutions. When we subjected these libraries to phosphorylation by the cAMP-dependent protein kinase, we obtained the optimal peptide sequence RRXS (I/L/V), in perfect agreement with the substrate sequence deduced from mutagenesis and crystal structure analyses. By using the same libraries, we showed that the optimal substrate peptide for both the type I and II TGF-beta receptors was KKKKKK(S/T)XXX. Since the two kinases are thought to play different roles in intracellular signal transduction, it was a surprise to find that they have almost identical substrate specificity. Our method is direct, sensitive, and simple and provides information about the kinase specificity for all the amino acid residues at each position.

Analysis of RNA-binding proteins by in vitro genetic selection: identification of an amino acid residue important for locking U1A onto its RNA target.

An in vitro genetic system was developed as a rapid means for studying the specificity determinants of RNA-binding proteins. This system was used to investigate the origin of the RNA-binding specificity of the mammalian spliceosomal protein U1A. The U1A domain responsible for binding to U1 small nuclear RNA was locally mutagenized and displayed as a combinatorial library on filamentous bacteriophage. Affinity selection identified four U1A residues in the mutagenized region that are important for specific binding to U1 hairpin II. One of these residues (Leu-49) disproportionately affects the rates of binding and release and appears to play a critical role in locking the protein onto the RNA. Interestingly, a protein variant that binds more tightly than U1A emerged during the selection, showing that the affinity of U1A for U1 RNA has not been optimized during evolution.

Genetic transfer of a nonpeptide antagonist binding site to a previously unresponsive angiotensin receptor.

Mutational analysis based on the pharmacological differences between mammalian and amphibian angiotensin II receptors (AT receptors) previously identified 7 aa residues located in transmembrane domains (TMs) III (Val-108), IV (Ala-163), V (Pro-192, Thr-198), VI (Ser-252), and VII (Leu-300, Phe-301) of the rat AT receptor type 1b (rAT1b receptor) that significantly influenced binding of the nonpeptide antagonist Losartan. Further studies have shown that an additional 6 residues in the rAT1b receptor TMs II (Ala-73), III (Ser-109, Ala-114, Ser-115), VI (Phe-248), and VII (Asn-295) are important in Losartan binding. The 13 residues required for Losartan binding in the mammalian receptor were exchanged for the corresponding amino acids in the Xenopus AT receptor type a (xATa receptor) to generate a mutant amphibian receptor that bound Losartan with the same affinity as the rAT1b receptor (Losartan IC50 values: rAT1b, 2.2 +/- 0.2 nM: xATa, > 50 microM; mutant, 2.0 +/- 0.1 nM). To our knowledge, this is the first report of a gain-of-function mutant in which the residues crucial to formation of a ligand binding site in a mammalian peptide hormone receptor were transferred to a previously unresponsive receptor by site-directed mutagenesis. Ala substitutions and comparison of mammalian and amphibian combinatorial mutants indicated that TM III in the rAT1b receptor plays a key role in Losartan binding. Identification of residues involved in nonpeptide ligand binding will facilitate studies aimed at elucidating the chemical basis for ligand recognition in the AT receptor and peptide hormone receptors in general.

Domains of transcription factor Sp1 required for synergistic activation with sterol regulatory element binding protein 1 of low density lipoprotein receptor promoter.

Feedback regulation of transcription from the low density lipoprotein (LDL) receptor gene is fundamentally important in the maintenance of intracellular sterol balance. The region of the LDL receptor promoter responsible for normal sterol regulation contains adjacent binding sites for the ubiquitous transcription factor Sp1 and the cholesterol-sensitive sterol regulatory element-binding proteins (SREBPs). Interestingly, both are essential for normal sterolmediated regulation of the promoter. The cooperation by Sp1 and SREBP-1 occurs at two steps in the activation process. SREBP-1 stimulates the binding of Sp1 to its adjacent recognition site in the promoter followed by enhanced stimulation of transcription after both proteins are bound to DNA. In the present report, we have defined the protein domains of Sp1 that are required for both synergistic DNA binding and transcriptional activation. The major activation domains of Sp1 that have previously been shown to be essential to activation of promoters containing multiple Sp1 sites are required for activation of the LDL receptor promoter. Additionally, the C domain is also crucial. This slightly acidic approximately 120-amino acid region is not required for efficient synergistic activation by multiple Sp1 sites or in combination with other recently characterized transcriptional regulators. We also show that Sp1 domain C is essential for full, enhanced DNA binding by SREBP-1. Taken together with other recent studies on the role of Sp1 in promoter activation, the current experiments suggest a unique combinatorial mechanism for promoter activation by two distinct transcription factors that are both essential to intracellular cholesterol homeostasis.

Codominance and toxins: a path to drugs of nearly unlimited selectivity.

The effectiveness of drugs is often limited by their insufficient selectivity. I propose designs of therapeutic agents that address this problem. The key feature of these reagents, termed comtoxins (codominance-mediated toxins), is their ability to utilize codominance, a property characteristic of many signals in proteins, including degradation signals (degrons) and nuclear localization signals. A comtoxin designed to kill cells that express intracellular proteins P1 and P2 but to spare cells that lack P1 and/or P2 is a multidomain fusion containing a cytotoxic domain and two degrons placed within or near two domains P1* and P2* that bind, respectively, to P1 and P2. In a cell containing both P1 and P2, these proteins would bind to the P1* and P2* domains of the comtoxin and sterically mask the nearby (appropriately positioned) degrons, resulting in a long-lived and therefore toxic drug. By contrast, in a cell lacking P1 and/or P2, at least one of the comtoxin's degrons would be active (unobstructed), yielding a short-lived and therefore nontoxic drug. A comtoxin containing both a degron and a nuclear localization signal can be designed to kill exclusively cells that contain P1 but lack P2. Analogous strategies yield comtoxins sensitive to the presence (or absence) of more than two proteins in a cell. Also considered is a class of comtoxins in which a toxic domain is split by a flexible insert containing binding sites for the target proteins. The potentially unlimited, combinatorial selectivity of comtoxins may help solve the problem of side effects that bedevils present-day therapies, for even nonselective delivery of a comtoxin would not affect cells whose protein "signatures" differ from the targeted one.

Human autoantibody recognition of DNA.

Combinatorial IgG Fab phage display libraries prepared from a systemic lupus erythematosus (SLE) donor and a healthy donor were affinity selected against human placental DNA. Human monoclonal antibody Fab fragments specific for DNA were isolated from both libraries, although Fabs of the highest affinity were isolated only from the lupus library. Generally, apparent affinities of the Fabs for human placental DNA, purified double-stranded DNA, and denatured DNA were approximately equivalent. Surface plasmon resonance indicated Fab binding constants for a double-stranded oligodeoxynucleotide of 0.2-1.3 x 10(8) M-1. The higher-affinity Fabs, as ranked by binding to human placental DNA or to the oligonucleotide probe, tested positive in the Crithidia luciliae assay commonly used in the diagnosis of SLE, and interestingly the genes encoding the heavy-chain variable regions of these antibodies displayed evidence of only minimal somatic hypermutation. The heavy chains of the SLE Fabs were characterized by a predominance of basic residues toward the N terminus of complementarity-determining region 3 (CDR3). The crucial role of heavy-chain CDR3 (HCDR3) in high-affinity DNA recognition was suggested by the creation of DNA binding in an unrelated antibody by HCDR3 transplantation from SLE antibodies. We propose that high-affinity DNA-binding antibodies can arise in SLE without extensive somatic hypermutation in the variable-region genes because of the expression of inappropriate HCDR3s.

Alterazione della proteostasi a livello del reticolo endoplasmatico: un potenziale target terapeutico nel carcinoma prostatico

Nel sesso maschile il carcinoma della prostata (CaP) è la neoplasia più frequente ed è tra le prime cause di morte per tumore. Ad oggi, sono disponibili diverse strategie terapeutiche per il trattamento del CaP, ma, come comprovato dall’ancora alta mortalità, spesso queste sono inefficaci, a causa soprattutto dello sviluppo di fenomeni di resistenza da parte delle cellule tumorali. La ricerca si sta quindi focalizzando sulla caratterizzazione di tali meccanismi di resistenza e, allo stesso tempo, sull’individuazione di combinazioni terapeutiche che siano più efficaci e capaci di superare queste resistenze. Le cellule tumorali sono fortemente dipendenti dai meccanismi connessi con l’omeostasi proteica (proteostasi), in quanto sono sottoposte a numerosi stress ambientali (ipossia, carenza di nutrienti, esposizione a chemioterapici, ecc.) e ad un’aumentata attività trascrizionale, entrambi fattori che causano un accumulo intracellulare di proteine anomale e/o mal ripiegate, le quali possono risultare dannose per la cellula e vanno quindi riparate o eliminate efficientemente. La cellula ha sviluppato diversi sistemi di controllo di qualità delle proteine, tra cui gli chaperon molecolari, il sistema di degradazione associato al reticolo endoplasmatico (ERAD), il sistema di risposta alle proteine non ripiegate (UPR) e i sistemi di degradazione come il proteasoma e l’autofagia. Uno dei possibili bersagli in cellule tumorali secretorie, come quelle del CaP, è rappresentato dal reticolo endoplasmatico (RE), organello intracellulare deputato alla sintesi, al ripiegamento e alle modificazioni post-traduzionali delle proteine di membrana e secrete. Alterazioni della protestasi a livello del RE inducono l’UPR, che svolge una duplice funzione nella cellula: primariamente funge da meccanismo omeostatico e di sopravvivenza, ma, quando l’omeostasi non è più ripristinabile e lo stimolo di attivazione dell’UPR cronicizza, può attivare vie di segnalazione che conducono alla morte cellulare programmata. La bivalenza, tipica dell’UPR, lo rende un bersaglio particolarmente interessante per promuovere la morte delle cellule tumorali: si può, infatti, sfruttare da una parte l’inibizione di componenti dell’UPR per abrogare i meccanismi adattativi e di sopravvivenza e dall’altra si può favorire il sovraccarico dell’UPR con conseguente induzione della via pro-apoptotica. Le catechine del tè verde sono composti polifenolici estratti dalle foglie di Camellia sinesis che possiedono comprovati effetti antitumorali: inibiscono la proliferazione, inducono la morte di cellule neoplastiche e riducono l’angiogenesi, l’invasione e la metastatizzazione di diversi tipi tumorali, tra cui il CaP. Diversi studi hanno osservato come il RE sia uno dei bersagli molecolari delle catechine del tè verde. In particolare, recenti studi del nostro gruppo di ricerca hanno messo in evidenza come il Polyphenon E (estratto standardizzato di catechine del tè verde) sia in grado, in modelli animali di CaP, di causare un’alterazione strutturale del RE e del Golgi, un deficit del processamento delle proteine secretorie e la conseguente induzione di uno stato di stress del RE, il quale causa a sua volta l’attivazione delle vie di segnalazione dell’UPR. Nel presente studio su due diverse linee cellulari di CaP (LNCaP e DU145) e in un nostro precedente studio su altre due linee cellulari (PNT1a e PC3) è stato confermato che il Polyphenon E è capace di indurre lo stress del RE e di determinare l’attivazione delle vie di segnalazione dell’UPR, le quali possono fungere da meccanismo di sopravvivenza, ma anche contribuire a favorire la morte cellulare indotta dalle catechine del tè verde (come nel caso delle PC3). Considerati questi effetti delle catechine del tè verde in qualità di induttori dell’UPR, abbiamo ipotizzato che la combinazione di questi polifenoli bioattivi e degli inibitori del proteasoma, anch’essi noti attivatori dell’UPR, potesse comportare un aggravamento dell’UPR stesso tale da innescare meccanismi molecolari di morte cellulare programmata. Abbiamo quindi studiato l’effetto di tale combinazione in cellule PC3 trattate con epigallocatechina-3-gallato (EGCG, la principale tra le catechine del tè verde) e due diversi inibitori del proteasoma, il bortezomib (BZM) e l’MG132. I risultati hanno dimostrato, diversamente da quanto ipotizzato, che l’EGCG quando associato agli inibitori del proteasoma non produce effetti sinergici, ma che anzi, quando viene addizionato al BZM, causa una risposta simil-antagonistica: si osserva infatti una riduzione della citotossicità e dell’effetto inibitorio sul proteasoma (accumulo di proteine poliubiquitinate) indotti dal BZM, inoltre anche l’induzione dell’UPR (aumento di GRP78, p-eIF2α, CHOP) risulta ridotta nelle cellule trattate con la combinazione di EGCG e BZM rispetto alle cellule trattate col solo BZM. Gli stessi effetti non si osservano invece nelle cellule PC3 trattate con l’EGCG in associazione con l’MG132, dove non si registra alcuna variazione dei parametri di vitalità cellulare e dei marcatori di inibizione del proteasoma e di UPR (rispetto a quelli osservati nel singolo trattamento con MG132). Essendo l’autofagia un meccanismo compensativo che si attiva in seguito all’inibizione del proteasoma o allo stress del RE, abbiamo valutato che ruolo potesse avere tale meccanismo nella risposta simil-antagonistica osservata in seguito al co-trattamento con EGCG e BZM. I nostri risultati hanno evidenziato, in cellule trattate con BZM, l’attivazione di un flusso autofagico che si intensifica quando viene addizionato l’EGCG. Tramite l’inibizione dell’autofagia mediante co-somministrazione di clorochina, è stato possibile stabilire che l’autofagia indotta dall’EGCG favorisce la sopravvivenza delle cellule sottoposte al trattamento combinato tramite la riduzione dell’UPR. Queste evidenze ci portano a concludere che per il trattamento del CaP è sconsigliabile associare le catechine del tè verde con il BZM e che in futuri studi di combinazione di questi polifenoli con composti antitumorali sarà importante valutare il ruolo dell’autofagia come possibile meccanismo di resistenza.

Solução rasterizada para o problema de empacotamento de fita irregular utilizando a Montanha Voronoi.

O empacotamento irregular de fita é um grupo de problemas na área de corte e empacotamento, cuja aplicação é observada nas indústrias têxtil, moveleira e construção naval. O problema consiste em definir uma configuração de itens irregulares de modo que o comprimento do contêiner retangular que contém o leiaute seja minimizado. A solução deve ser válida, isto é, não deve haver sobreposição entre os itens, que não devem extrapolar as paredes do contêiner. Devido a aspectos práticos, são admitidas até quatro orientações para o item. O volume de material desperdiçado está diretamente relacionado à qualidade do leiaute obtido e, por este motivo, uma solução eficiente pressupõe uma vantagem econômica e resulta em um menor impacto ambiental. O objetivo deste trabalho consiste na geração automática de leiautes de modo a obter níveis de compactação e tempo de processamento compatíveis com outras soluções na literatura. A fim de atingir este objetivo, são realizadas duas propostas de solução. A primeira consiste no posicionamento sequencial dos itens de modo a maximizar a ocorrência de posições de encaixe, que estão relacionadas à restrição de movimento de um item no leiaute. Em linhas gerais, várias sequências de posicionamentos são exploradas com o objetivo de encontrar a solução mais compacta. Na segunda abordagem, que consiste na principal proposta deste trabalho, métodos rasterizados são aplicados para movimentar itens de acordo com uma grade de posicionamento, admitindo sobreposição. O método é baseado na estratégia de minimização de sobreposição, cujo objetivo é a eliminação da sobreposição em um contêiner fechado. Ambos os algoritmos foram testados utilizando o mesmo conjunto de problemas de referência da literatura. Foi verificado que a primeira estratégia não foi capaz de obter soluções satisfatórias, apesar de fornecer informações importantes sobre as propriedades das posições de encaixe. Por outro lado, a segunda abordagem obteve resultados competitivos. O desempenho do algoritmo também foi compatível com outras soluções, inclusive em casos nos quais o volume de dados era alto. Ademais, como trabalho futuro, o algoritmo pode ser estendido de modo a possibilitar a entrada de itens de geometria genérica, o que pode se tornar o grande diferencial da proposta.

A memetic algorithm for the delineation of local labour markets

Given a territory composed of basic geographical units, the delineation of local labour market areas (LLMAs) can be seen as a problem in which those units are grouped subject to multiple constraints. In previous research, standard genetic algorithms were not able to find valid solutions, and a specific evolutionary algorithm was developed. The inclusion of multiple ad hoc operators allowed the algorithm to find better solutions than those of a widely-used greedy method. However, the percentage of invalid solutions was still very high. In this paper we improve that evolutionary algorithm through the inclusion of (i) a reparation process, that allows every invalid individual to fulfil the constraints and contribute to the evolution, and (ii) a hillclimbing optimisation procedure for each generated individual by means of an appropriate reassignment of some of its constituent units. We compare the results of both techniques against the previous results and a greedy method.

Grouping genetic operators for the delineation of functional areas based on spatial interaction

The delineation of functional economic areas, or market areas, is a problem of high practical relevance, since the delineation of functional sets such as economic areas in the US, Travel-to-Work Areas in the United Kingdom, and their counterparts in other OECD countries are the basis of many statistical operations and policy making decisions at local level. This is a combinatorial optimisation problem defined as the partition of a given set of indivisible spatial units (covering a territory) into regions characterised by being (a) self-contained and (b) cohesive, in terms of spatial interaction data (flows, relationships). Usually, each region must reach a minimum size and self-containment level, and must be continuous. Although these optimisation problems have been typically solved through greedy methods, a recent strand of the literature in this field has been concerned with the use of evolutionary algorithms with ad hoc operators. Although these algorithms have proved to be successful in improving the results of some of the more widely applied official procedures, they are so time consuming that cannot be applied directly to solve real-world problems. In this paper we propose a new set of group-based mutation operators, featuring general operations over disjoint groups, tailored to ensure that all the constraints are respected during the operation to improve efficiency. A comparative analysis of our results with those from previous approaches shows that the proposed algorithm systematically improves them in terms of both quality and processing time, something of crucial relevance since it allows dealing with most large, real-world problems in reasonable time.

Global behavior of the Douglas–Rachford method for a nonconvex feasibility problem

In recent times the Douglas–Rachford algorithm has been observed empirically to solve a variety of nonconvex feasibility problems including those of a combinatorial nature. For many of these problems current theory is not sufficient to explain this observed success and is mainly concerned with questions of local convergence. In this paper we analyze global behavior of the method for finding a point in the intersection of a half-space and a potentially non-convex set which is assumed to satisfy a well-quasi-ordering property or a property weaker than compactness. In particular, the special case in which the second set is finite is covered by our framework and provides a prototypical setting for combinatorial optimization problems.

Controlling Hox gene expression and activity to build the vertebrate axial skeleton

It has long been known that Hox genes are central players in patterning the vertebrate axial skeleton. Extensive genetic studies in the mouse have revealed that the combinatorial activity of Hox genes along the anterior-posterior body axis specifies different vertebral identities. In addition, Hox genes were instrumental for the evolutionary diversification of the vertebrate body plan. In this review, we focus on fundamental questions regarding the intricate mechanisms controlling Hox gene activity. In particular, we discuss the functional relevance of the precise timing of Hox gene activation in the embryo. Moreover, we provide insight into the epigenetic regulatory mechanisms that are likely to control this process and are responsible for the maintenance of spatially restricted Hox expression domains throughout embryonic development. We also analyze how specific features of each Hox protein may contribute to the functional diversity of Hox family. Altogether, the work reviewed here further supports the notion that the Hox program is far more complex than initially assumed. Exciting new findings will surely emerge in the years ahead.

On the ordering, enumeration and ranking of k-ary trees /

"UILU-ENG 77 1706."

Computing a perfect strategy for n x [i.e. superscript] n chess requires time exponential in n /

"UILU-ENG 79 1716."

Sperner's theorem on maximal-sized antichains and its generation /

Includes bibliographical references.