New Software Models Immune Responses

ScienceDaily (Oct. 9, 2011) — Researchers with the Virginia Bioinformatics Institute at Virginia Tech have released an upgrade to the institute's ENteric Immunity SImulator (ENISI) software, which models immune responses to beneficial and harmful bacteria that enter the gastrointestinal tract of mice, pigs, and humans. ENISI allows users to create enteric systems such as the gut-associated mucosal immune system in silico, providing a better glimpse of how the immune system responds to pathogens that invade the bacteria-rich environment of the gut.

ENteric Immunity SImulator software created at Virginia Bioinformatics Institute at Virginia Tech allows researchers to model gut responses to various bacteria. 

ENISI was initially designed by the Center for Modeling Immunity to Enteric Pathogens (MIEP) to model inflammatory bowel disease. The upgrade allows investigators to simulate immune responses in a mouse infected with Helicobacter pylori. The MIEP team plans to expand the software to simulate infection with enteroaggregative Escherichia coli and other enteric pathogens, such as Clostridium difficile and Cryptosporidium parvum. Future upgrades will allow users to run simulations via the ENISI website and eventually be able to visualize in silico cells or lesions forming in real time, rather than only seeing the outcomes of such interactions.

"ENISI is unique because it's specific to the gut, simulating each individual cell rather than creating broad mathematical models," said Kate Wendelsdorf, a Ph.D. student in the genetics, bioinformatics, and computational biology program at Virginia Tech. "Thus, it's more faithful to a living system and allows us to simulate a million individual cells, more than any other simulator. It's a powerful tool for understanding interactions between gut pathogens and the mucosal immune system."

Researchers can manipulate cells and immune processes in ENISI to determine if, for example, blocking a specific immune pathway or adding a drug can inhibit pathogen invasion and infection. The computer-generated models can, in turn, help researchers design better experiments to test the simulations in laboratory settings or in live animals. Therefore, it may be possible to test the efficacy of a novel vaccine or immune therapeutic in an ENISI model of disease, confirm the results in an animal model, and then use those results to explore the mechanisms of therapeutic efficacy in additional studies.

This feature will help immunologists and infectious disease experts immensely in understanding pathology, diagnosis, and treatment.

"ENISI is based on an interaction-based modeling approach that represents individual cells and their interactions with other cells, pathogens, and the environment. The algorithmic/procedural representation of individual agents and their interactions with other agents via an abstract interaction network is central to the modeling process. The use of high-performance computing facilitates scaling to 106 cells; we expect this number to grow 100-fold over the next two years. Such a representation yields a fundamentally different approach to understanding novel immunological processes," said Madhav Marathe, the center's modeling lead.

"ENISI runs on high-performance computers: hundreds or thousands of servers working together to produce an answer. The program shows the power of trans-disciplinary science, bringing together a team of software developers, computer scientists, immunologists, and physicists to solve problems that they wouldn't have been able to tackle on their own," said Keith Bisset, modeling expert and a key developer of the ENISI software.

A Center for Modeling Immunity to Enteric Pathogens paper entitled, "Enteric Immunity Simulator: A tool for in silico study of gut immunopathologies," has been accepted in the IEEE Bioinformatics and Biomedicine (BIBM) International conference proceedings. Preliminary ENISI modeling results that simulate bacterial-induced colitis will be presented at the conference in Atlanta in November.

"One of our goals is to develop user-friendly and interactive modeling tools that engage and inform the immunology and infectious disease communities, thereby enabling paradigm-shifting scientific discovery," said Josep Bassaganya-Riera, the center's principal investigator. "The release of the upgraded ENISI software by the MIEP team is a major step in allowing powerful computer simulations to uncover novel mechanisms of immunoregulation underlying immune responses to gut pathogens. The ultimate goal of such powerful simulations is to accelerate the discovery of novel drug targets and biomarkers for enteric infectious diseases. The fully integrated computational modeling, bioinformatics and immunology experimentation efforts within the MIEP program enable the generation of mechanistic evidence in silico and efficient validation in vivo," and Bassaganya-Riera, who is also director of the Nutritional Immunology and Molecular Medicine Laboratory at Virginia Bioinformatics Institute.

Clonagem humana gera células-tronco embrionárias

Clonagem Humana

Cientistas afirmam ter criado células-tronco humanas por meio de clonagem.

Essencialmente, a técnica envolve pegar um óvulo humano e combiná-lo com uma célula de outra pessoa adulta, sem retirar o DNA original da célula.

Esta área de pesquisas é altamente controversa, não apenas por suas implicações éticas, mas também por causa de uma fraude científica recente.

Em 2004, o cientista sul-coreano Hwang Woo-suk ganhou fama meteórica ao anunciar que teria produzido uma linhagem de células-tronco geradas a partir do embrião de um clone humano.

Como todo bom meteoro, Hwang queimou-se na atmosfera quando se descobriu que ele tinha forjado resultados, além de ter obtido os óvulos de forma antiética e ilegal.

Preservando o DNA

Agora, Scott Noggle, Dieter Egli e seus colegas do Laboratório da Fundação de Células-Tronco de Nova Iorque (EUA), anunciaram, em um artigo publicado na revista Nature, ter alcançado resultados intermediários, mas por uma via diferente.

Eles usaram uma tecnologia de clonagem chamada transferência de núcleos de célula somática.

A técnica mais comum de clonagem consiste na remoção do núcleo de um óvulo e sua substituição pelo núcleo da célula do doador, cujo DNA é então inserido no óvulo inicial. Imerso em nutrientes, o óvulo se divide, passando então por uma reprogramação genética, assumindo o DNA do doador.

Na nova técnica, o DNA do óvulo é mantido, recebendo o material genético de células epiteliais de um doador adulto.

"Pode ser um bom momento para as Nações Unidas começarem a forjar regulamentações ou restrições sobre a clonagem, que têm estado paralisadas pelo debate político e religioso," afirma a revista Nature em editorial. "[E] pacientes desesperados vão encontrar médicos prontos a lhes dar tratamentos com células-tronco embrionárias não-comprovados e inseguros."[Imagem: Noggle et al./Nature]

Células-tronco embrionárias clonadas

O resultado é uma célula triploide, com três pares de cromossomos: 23 do óvulo original e 46 (dois pares de 23) da célula do doador - teoricamente um embrião inviável, embora ele não tenha sido deixado para se desenvolver.

O óvulo se desenvolveu até o estágio conhecido como blastocisto, composto por cerca de 100 células.

O blastocisto é usado como fonte de células-tronco embrionárias, usadas em inúmeras pesquisas e vistas como um recurso futuro para a cura de várias doenças.

Os cientistas afirmam ter visto nas células do embrião triploide indícios de células-tronco embrionárias normais, o que comprovaria a importância de se manter o DNA original do óvulo.

Isto também pode ser uma demonstração de que as chamadas "técnicas tradicionais" de clonagem não são eficientes como se acreditava.

Células-tronco personalizadas

A clonagem é um recurso idealizado para evitar o problema da rejeição que ocorre quando um paciente recebe células-tronco de um doador.

Neste caso, o sistema imunológico do receptor vê as células-tronco como invasoras, exigindo o uso de imunossupressores, o que complica e pode até inviabilizar o tratamento.

Com a clonagem, torna-se teoricamente possível criar "células-tronco personalizadas", criadas com o próprio DNA do receptor, evitando então o problema da rejeição.

Ética na clonagem

A pesquisa está em um passo bastante inicial. Um editorial da revista Nature, onde a pesquisa foi publicada, afirma que os embriões triploides são geneticamente anômalos e inviáveis.

Os pesquisadores vão precisar ainda produzir um embrião diploide, com 46 cromossomos, antes de pensar em usar terapeuticamente as células-tronco clonadas.

Se eles conseguirem, recomeçará então todo o debate ético sobre o que fazer com estes embriões, até que ponto eles poderão ser deixados crescer, e se será permitida a realização da clonagem reprodutiva.

"Pode ser um bom momento para as Nações Unidas começarem a forjar regulamentações ou restrições sobre a clonagem, que têm estado paralisadas pelo debate político e religioso," afirma a revista Nature em editorial. "[E] pacientes desesperados vão encontrar médicos prontos a lhes dar tratamentos com células-tronco embrionárias não-comprovados e inseguros."

Lipoaspiração sem exercícios pode ser perigosa

Gordura visceral

A realização da lipoaspiração não acompanhada de atividade física regular no pós-operatório pode acarretar um aumento significativo da gordura visceral, localizada na região entre os órgãos.

Essa gordura é extremamente danosa para a saúde por estar associada ao aumento do risco cardiovascular.

Os exercícios físicos inibem o aumento dessa gordura entre os órgãos - veja Gordura abdominal interna é a mais perigosa para doenças do coração.

A conclusão é de um estudo realizado na Escola de Educação Física e Esporte (EEFE) da Universidade de São Paulo (USP).

Treinadas e sedentárias

A pesquisadora Fabiana Braga Benatti recrutou 36 mulheres com Índice de Massa Corporal (IMC) abaixo de 30, que fariam lipoaspiração na região abdominal, para participar da pesquisa.

O IMC é calculado a partir do peso da pessoa em quilogramas, dividido pela sua altura em metros elevada ao quadrado.

O grupo foi igualmente dividido em "mulheres treinadas" e "mulheres sedentárias".

Dois meses depois da cirurgia, o primeiro grupo foi submetido à uma série de exercícios de força e aeróbicos, por três vezes semanais, durante quatro meses, enquanto o segundo grupo permaneceu sem fazer atividades físicas regulares.

Uma bateria de exames foi feita antes e depois do processo e serviu de base para toda a pesquisa.

Aumento de gordura sem perceber

No grupo das mulheres sedentárias, o ganho da massa visceral chegou a 10%.

O fato não foi percebido pelas pacientes, pois o aumento desta gordura interna do corpo dificilmente é identificado no dia-a-dia, já que não representa grandes proporções em termos visuais.

Isso aumenta a importância do estudo, já que dificilmente estes dados seriam alcançados a não ser por um acompanhamento detalhado durante o pós-operatório.

Já no grupo de mulheres treinadas não houve aumento da gordura visceral. O treinamento físico preveniu este aumento.

Uma possível explicação para isso é o fato deste tipo de gordura ser metabolicamente ativo e mais responsivo ao aumento das concentrações de adrenalina que ocorrem durante o exercício físico.

Além disso, o treinamento físico preservou o gasto energético das mulheres treinadas, o que pode ter contribuído para seus efeitos benéficos observados.

Lipoaspiração não é para perder peso

O peso perdido na cirurgia de lipoaspiração foi recuperado em ambos os grupos.

"A cirurgia não tem como objetivo a redução de peso, que diminui em média 1%. A pretensão da lipoaspiração é retirar a gordura localizada e modelar o corpo do paciente", diz Fabiana.

No caso das mulheres sedentárias, contudo, o peso retornou possivelmente pelo novo ganho de massa gorda, favorecida pelo estilo de vida levado. O metabolismo se esforça para manter uma constante e isso inclui o peso.

Perda de massa gorda

A diminuição do gasto energético durante dietas restritivas normalmente é atribuída à perda de massa magra.

"Como não se percebeu perda de massa magra durante o estudo, este resultado foi considerado inesperado. "Acreditamos que tenha a ver com a perda de massa gorda", diz Fabiana.

A retirada de massa gorda ocasiona, ainda, a queda nos níveis do hormônio adiponectina, que tem efeito benéfico no corpo. Ele regula a sensibilidade da insulina que, quando alterada, pode gerar uma série de consequências danosas para o corpo, a mais conhecida delas sendo a diabetes.

Puramente estético

Ao contrabalancear os efeitos da lipoaspiração, Fabiana diz que o que deve ser feito é um esclarecimento sobre os efeitos colaterais causados pela cirurgia.

"Metabolicamente falando, não vimos nada de benéfico na cirurgia. Ela é um procedimento puramente estético", conclui.

O aumento da gordura visceral e dos riscos que isso traz podem ser evitados, mas para isso é preciso atentar e esclarecer, tanto para médicos quanto para pacientes, a real necessidade de fixação de uma série de exercícios na rotina do pós-operatório.

• Suplemento alimentar só reduz peso se acompanhado de exercício

MVA-B Spanish HIV Vaccine Shows 90 Percent Immune Response in Humans

ScienceDaily (Oct. 6, 2011) — Phase I clinical trials developed by Spanish Superior Scientific Research Council (CSIC) together with Gregorio Marañón Hospital in Madrid and Clínic Hospital in Barcelona, reveals MVA-B preventive vaccine's immune efficiency against human immunodeficiency virus (HIV). 90% of the volunteers who went through the tests developed an immunological response against the virus and 85% has kept this response for at least one year. Safety and efficiency of this treatment have been described in articles for Vaccine and theJournal of Virology.

Three-dimensional model of an HIV particle. 

The success of this vaccine, CSIC's patent, is based on the capability of human's immune system to learn how to react over time against virus particles and infected cells. "MVA-B vaccine has proven to be as powerful as any other vaccine currently being studied, or even more," says Mariano Esteban, head researcher from CSIC's National Biotech Centre.

In 2008, MVA-B already showed very high efficiency in mice as well as macaque monkeys against Simian's immunodeficiency virus (SIV). Due to it's high immunological response in humans, Phase I clinic trials will be conducted with HIV infected volunteers, to test its efficiency as a therapeutic vaccine.

Weapon's origins

Back in 1999, Esteban's research team began to work in the development and preclinical studies of MVA-B, which name comes from its composition, based in Modified Ankara Vaccinia virus. MVA-B is an attenuated virus, which has already been used in the past to eradicate smallpox, and also as a model in the research of many other vaccines. The "B" stands for the HIV subtype it is meant to work against, the most common in Europe.

Development of MVA-B is based in the insertion of four HIV genes (Gag, Pol, Nef & Env) in Vaccina's genetic sequence. A healthy immunitary system is able to react against MVA.

On the other hand, the inserted HIV genes in its DNA are not able to self-replicate, which guarantees the safety of the clinical trial.

30 healthy volunteers participated in this clinical trial. 24 of them were treated with MVA-B, while the other 6 were treated with a placebo, following a double-blind testing method. 3 doses of the vaccine were given via intramuscular route in weeks 0, 4 and 16. The effects were studied in peripheral blood until the trial ended on week 48.

Combat battalion

Inoculating the vaccine in a healthy volunteer is intended to train it's immune system to detect and learn how to combat those virus components. According to Esteban " it is like showing a picture of the HIV so that it is able to recognise it if it sees it again in the future."

Lymphocytes T and B are the main cells in this experiment, the soldiers in charge of detecting the foreign substances in the body and sending the right coordinates to destroy them.

"Our body is full of lymphocytes, each of them programmed to fight against a different pathogen" says Esteban. For that reason "Training is needed when it involves a pathogen, like the HIV one, which cannot be naturally defeated."

Lymphocytes B are responsible for the humoral immune response, producing antibodies which attack the HIV particles before they penetrate and infect the cell, anchoring themselves to the external structure and blocking it. 48th week blood tests reveal 72,7% of the treated volunteers hold specific antibodies against HIV.

On the other side, lymphocytes T control cell's immune response, in charge of detecting and destroying HIV infected cells. In order to verify their defence response to the vaccine, production of interferon gamma immunitary protein was measured.

Tests performed on the 48th week, 32 weeks after the last inoculation of the vaccine, show the production of lymphocytes T CD4+ and CD8+ of the vaccinated group is 38,5% and 69,2%, respectively, while it stays at 0% in the control group.

Action in several fronts

Besides interferon gamma, other immune proteins (cytokines and chemokines) are produced by the body when the presence of a pathogen is detected. Each of these proteins tends to attack a different enemy front. When T lymphocytes' defence action is able to generate several of these proteins it is called a polyfunctional action. CSIC's researcher adds "The importance of polyfunctionality has to do with the capability of pathogens to develop resistance to the immune systems attacks. The higher the polyfunctionality, the lower the resistance."

The defence spectrum of T lymphocytes in vaccinated subjects was measured based on the production of 3 other immunitary proteins. Tests indicate the vaccine generates up to 15 types of lymphocyte T CD4+ and CD8+ populations. 25% of CD4+ type and 45% of CD8+ type are able to produce two or more different proteins, proving their polyfunctionality.

War veterans

For a vaccine to become really effective, besides its immune system's defence capability, generating a long lasting response against future attacks is the key. For this purpose, the body needs to be able to keep a basic level of memory T lymphocytes. These lymphocytes, generated after a first pathogen attack, are veteran soldiers, which can circulate the body for years, prepared to respond to a new enemy's incursion.

48th week blood tests ran on vaccinated subjects show over 50% of CD4+ and CD8+ lymphocytes were memory T lymphocytes in the 85% of the patients who kept an immune response at this point of the trials.

In Esteban's opinión "MVA-B immune profile meets, initially, the requirements for a promising HIV vaccine." MVA-B is not capable of removing the virus from the body as once a cell is infected, virus' genetic data is integrated and replicated with the cell. However, the immune response induced by the vaccine could keep the virus under control, "if the virus enters the body and tries to develop in a cell, the immune system is ready to inactivate the virus and destroy the infected cell."

According to CSIC's researcher: "If this genetic cocktail passes Phase II and Phase III future clinic trials, and makes it into production, in the future HIV could be compared to herpes virus nowadays." Virus would not cause a disease anymore and would become a minor chronic infection, which would only show its effects in a low defence scenario, with a much lower contagious profile.

Evidence Found for the Genetic Basis of Autism: Models of Autism Show That Gene Copy Number Controls Brain Structure and Behavior

ScienceDaily (Oct. 6, 2011) — Scientists at Cold Spring Harbor Laboratory (CSHL) have discovered that one of the most common genetic alterations in autism -- deletion of a 27-gene cluster on chromosome 16 -- causes autism-like features. By generating mouse models of autism using a technique known as chromosome engineering, CSHL Professor Alea Mills and colleagues provide the first functional evidence that inheriting fewer copies of these genes leads to features resembling those used to diagnose children with autism.

This three-dimensional representation of the mouse brain highlights eight regions (shown with different colors) affected by 16.p11.2 deletion. 

The study appears in theProceedings of the National Academy of Sciences in the early online edition during the week of October 3.

"Children normally inherit one copy of a gene from each parent. We had the tools to see whether copy number changes found in kids with autism were causing the syndrome," explains Mills. In 2007, Professor Michael Wigler, also at CSHL, revealed that some children with autism have a small deletion on chromosome 16, affecting 27 genes in a region of our genomes referred to as 16p11.2. The deletion -- which causes children to inherit only a single copy of the 27-gene cluster -- is one of the most common copy number variations (CNVs) associated with autism.

"The idea that this deletion might be causing autism was exciting," says Mills. "So we asked whether clipping out the same set of genes in mice would have any effect."

After engineering mice that had a chromosome defect corresponding to the human 16p11.2 deletion found in autism, Mills and her team analyzed these models for a variety of behaviors, as the clinical features of autism often vary widely from patient to patient, even within the same family.

"Mice with the deletion acted completely different from normal mice," explains Guy Horev, a Postdoctoral Fellow in the Mills laboratory and first author of the study. These mice had a number of behaviors characteristic of autism: hyperactivity, difficulty adapting to a new environment, sleeping deficits, and restricted, repetitive behaviors.

Interestingly, mice that had been engineered to carry an extra copy, or duplication, of the 16p11.2 region did not have these characteristics, but instead, had the reciprocal behaviors. For each behavior, the deletion had a more dire consequence than the duplication, indicating that gene loss was more severe. This might explain why 16p11.2 duplications are detected much more frequently than deletions within the human population, and why patients with 16p11.2 deletions tend to be diagnosed earlier than those with duplications.

The mouse models also revealed a potential link between 16p11.2 deletion and survival, as about half the mice died following birth. Whether these findings extend to the human population might be answered by future studies that investigate the link between this deletion and unexplained cases of infant death.

The researchers also used MRI to identify specific regions of the brain that were altered in the autism models, revealing that eight different parts of the brain were affected. The group is now working to identify which gene or group of genes among the 27 that are located within the deleted region is responsible for the behaviors and brain alterations observed.

"Alea Mills has created a valuable resource for everyone engaged in autism research. The technical skill is extraordinary in creating mouse models bearing a human genetic variant that has been associated with autism," says Dr. Gerald Fischbach, Director of Life Sciences and Simons Foundation Autism Research Initiative (SFARI).

These mice will be invaluable for pinpointing the genetic basis of autism and for elucidating how these alterations affect the brain. They could also be used for inventing ways to diagnose children with autism before they develop the full-blown syndrome, as well as for designing clinical interventions.

Collaborators on this work include a group of MRI specialists led by Dr. Mark Henkelman at the Hospital of Sick Children in Toronto. This study was funded by the Simons Foundation Autism Research Initiative (SFARI).