Clutter cutter: Computer modeling used to understand how messy cells contribute to cancer

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Life can be messy at all scales, requiring different organizational strategies — from cleaning the house, to removing damaged or expired cells from the body to avoid cancer progression.In a messy house, people use computers to manage paper and photo clutter; companies use computer systems to track their inventory. Now a team of researchers at Vanderbilt University in Nashville, Tenn., is taking a similar approach to cell-molecular inventory control for cancer. They have created computer models, using their programming framework (PySB), which enable them to explore the complex biochemical processes that drive cancer growth.”Our hypothesis is that understanding how the cell uses their protein inventory will lead to understanding why cells dysregulate and become carcinogenic. We expect model outputs will lead to novel, targeted cancer therapies — possibly by 2019,” explained researcher Carlos F. Lopez, who will present the work at the 58th annual Biophysical Society Meeting in San Francisco, Feb.15-19.Lopez is interested in understanding how cells in multicellular organisms engage programmed cell death — so-called “cell suicide” — for cellular removal. It is a natural part of many cells’ life cycle.When cancer cells avoid programmed cell death, uncontrolled growth fuels tumor progression. The Vanderbilt team expects their computer models to identify what goes wrong in these cases, at a speed and scale never before possible. Lopez noted: “We are bridging the nanoscale molecular-level biochemical interactions with the macroscale cancer tumor outcomes, which is a huge range in scales. Most people don’t realize this, but molecular chemical reactions at the nanometer and nanosecond level affect things that happen at the timescale level of years — nine orders of magnitude in space and time! For comparison, a nanosecond is to a second like a second is to one century.”Rather than listing the cellular biochemical reactions by hand, PySB enables the researchers to “write” the biochemical cellular processes as computer programs. …


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#Agriculture, #Alzheimer, #Body, #Carlos, #Cell, #Inventory, #Lopez, #Processes, #Protein, #Researchers, #Result, #University

How gut bacteria communicate within our bodies, build special relationship

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Communication is vital to any successful relationship. Researchers from the Institute of Food Research and the University of East Anglia have discovered how the beneficial bacteria in our guts communicate with our own cells.This is a key step in understanding how our bodies maintain a close relationship with the population of gut bacteria that plays crucial roles in maintaining our health, fighting infection and digesting our food.A study, published in the journal Cell Reports, shows that the gut bacteria produce an enzyme that modifies signalling in cells lining the gut. The enzyme also has another role in breaking down food components.”Our study provides a breakthrough in understanding how bacteria communicate across different kingdoms to influence our own cells’ behavior, as well as how we digest our food,” said Dr Regis Stentz from the IFR, which is strategically funded by the Biotechnology and Biological Sciences Research Council.We all rely on trillions of bacteria in our gut to break down certain components of our diet. One example is phytate, the form phosphorus takes in cereals and vegetables. Broken down phytate is a source of vital nutrients, but in its undigested form it has detrimental properties. It binds to important minerals preventing them being taken up by the body, causing conditions like anemia, especially in developing countries. Phytate also leads to excess phosphorus leaching into the soil from farm animal waste, and feed supplements are used to minimize this.But despite the importance of phytate, we know very little about how it is broken down in our gut. To address this Dr Stentz and colleagues screened the genomes of hundreds of different species of gut bacteria. They found, in one of the most prominent gut bacteria species, an enzyme able to break down phytate. In collaboration with Norwich Research Park colleagues at the University of East Anglia, they crystallized this enzyme and solved its 3D structure. …


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#Alternative-Medicine, #Anglia, #Biological, #Body, #Ecology, #Health, #Professor, #Research, #Sciences, #Stentz, #University

The number of tumor cells spread to sentinel lymph nodes affects melanoma prognosis

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Cancer cell spread to the sentinel node — the lymph node to which cancer cells are most likely to spread from a primary tumor — is a risk factor for melanoma death. According to a study published in this week’s PLOS Medicine by Anja Ulmer, Christoph Klein and colleagues from the Universities of Tbingen and Regensburg, Germany, the prognosis of a patient largely depends on the number of disseminated cancer cells per million lymphocytes in the sentinel node. Even very low numbers were found to be predictive for reduced survival.The leading cause of death from skin disease is melanoma, which is the most dangerous type of skin cancer. When melanoma metastasizes and spreads to other parts of the body, treatment options become limited and the prognosis is poor. Melanoma staging (and prognosis) is currently focused on the primary tumor itself, with characteristics like tumor thickness, mitotic rate, and ulceration (break in the skin caused by the tumor) indicating the likelihood that the tumor has started to spread. Looking for tumor cells in the sentinel nodes is done for patients who are at increased risk for spread, but standard procedures for how to measure spread to the nodes and how to integrate this information with the tumor histology are needed. Since melanoma is one of the deadliest cancers, better predictors of prognosis for melanoma patients are needed for patient information and to determine treatment options.The researchers prospectively collected a large number of samples for this relatively rare cancer: 1,834 sentinel lymph nodes from 1,027 patients with melanoma who had been followed for 5 years after the samples were taken. They labelled disseminated cancer cells (DCCs) in the lymph nodes through the use of a marker for melanoma cells, counted them, and calculated DCC density. They then asked whether DCC density was related to a patient’s survival. They found that patients with high DCC density in the lymph nodes were more likely to die from melanoma within 5 years. …


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#Agriculture, #Alzheimer, #Body, #Christophklein, #Current, #Disease, #Health, #King, #Medicine, #Plos, #Standard, #Tbingen

Scientists chip away at mystery of what lives in our mouths

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Scientists have pieced together sections of DNA from 12 individual cells to sequence the genome of a bacterium known to live in healthy human mouths.With this new data about a part of the body considered “biological dark matter,” the researchers were able to reinforce a theory that genes in a closely related bacterium could be culprits in its ability to cause severe gum disease.Why the dark matter reference? More than 60 percent of bacteria in the human mouth refuse to grow in a laboratory dish, meaning they have never been classified, named or studied. The newly sequenced bacterium, Tannerella BU063, is among those that to date have not successfully been grown in culture — and its genome is identified as “most wanted” by the Human Microbiome Project.The federal Human Microbiome Project aims to improve research about the microbes that play a role in health and disease. Those 12 cells of BU063 are a good example of the complexity of life in the mouth: They came from a single healthy person but represented eight different strains of the bacterium.BU063 is closely related to the pathogen Tannerella forsythia, a bacterium linked to the gum disease periodontitis. Despite being “cousins,” this research revealed that they have clear differences in their genetic makeup.Those genes lacking in BU063 but present in forsythia — meaning they are a likely secret behind forsythia’s virulence — are now identified as good targets for further study, researchers say.”One of the tantalizing things about this study was the ability to do random searches of other bacteria whose levels are higher in periodontitis,” said Clifford Beall, research assistant professor of oral biology at The Ohio State University and lead author of the study. “We looked for genes that were present in these bacteria and forsythia and not in BU063. There is one particular gene complex in a whole list of these periodontitis-related bacteria that could be involved with virulence.”The research is published in the journal PLOS ONE.Periodontitis results when extensive inflammation or infection of the gums spreads beyond the gums to damage structures that support the teeth, including bone. Pockets that form between the gums and teeth are filled with different kinds of bacteria. Treatment typically involves deep cleaning or surgery to remove these infected pockets. Because multiple bacteria are associated with the disease, antibiotics have not been considered effective for treatment.And though many bacteria in these pockets have been collected and at least partially identified, their characteristics remain a mystery.”We think some of the gene differences we’ve found in this study are important, but it’s still not clear what all these genes do, meaning we still don’t know why certain bacteria in periodontitis are pathogenic in the first place. …


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#Body, #Dna, #Federal, #Gene, #Health, #State, #Study, #University

Embryology: Scientists crack open "black box" of development and see a "rosette"

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We know much about how embryos develop, but one key stage — implantation — has remained a mystery. Now, scientists from Cambridge have discovered a way to study and film this ‘black box’ of development. Their results — which will lead to the rewriting of biology text books worldwide — are published in the journal Cell.Embryo development in mammals occurs in two phases. During the first phase, pre-implantation, the embryo is a small, free-floating ball of cells called a blastocyst. In the second, post-implantation, phase the blastocyst embeds itself in the mother’s uterus.While blastocysts can be grown and studied outside the body, the same has not been true from implantation. And because embryos are so closely connected to their mothers, implantation has also been difficult to study in the womb.According to study author Professor Magdalena Zernicka-Goetz of the University of Cambridge: “We know a lot about pre-implantation, but what happens after implantation — and particularly the moment of implantation — is an enigma.”Scientists are interested in studying implantation because the embryo undergoes huge changes in such a short space of time.”During these two days, it goes from a relatively simple ball to a much larger, more complex cup-like structure, but exactly how that happens was a mystery — a black box of development. That is why we needed to develop a method that would allow us to culture and study embryos during implantation,” she explained.Working with mouse cells, Professor Zernicka-Goetz and her colleague Dr Ivan Bedzhov succeeded in creating the right conditions outside the womb to study the implantation process.To be able to support development, they created a system comprising a gel and medium that, as well as having the right chemical and biological properties, was of similar elasticity to uterine tissue. Crucially, this gel was transparent to optical light, allowing then to film the embryo during implantation.This new method revealed that on its way from ball to cup, the blastocyst becomes a ‘rosette’ of wedge-shaped cells, a structure never before seen by scientists.”It’s a beautiful structure. This rosette is what a mouse looks like on the 4th day of its life, and most likely what we look like on the 7th day of ours, and it’s fascinating how beautiful we are then, and how these small cells organise so perfectly to allow us to develop.”As well as answering a fundamental question in developmental biology, the new method will allow scientists to study embryo growth and development at implantation for the first time, which could help improve the success of IVF, and extend our knowledge of stem cells, which could advance their use in regenerative medicine.The findings also mean developmental biology text books will need rewriting. “The text books make an educated guess of what happened during this part of development, but we now know that what I learned and what I teach my students about this was totally wrong,” said Professor Zernicka-Goetz.Story Source:The above story is based on materials provided by University of Cambridge. …


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#Biology, #Body, #Cambridge, #Development, #Ecology, #Goetz, #Journal, #King, #Pregnancy, #Science, #Scientists, #Zernicka

"Sexy" underwear is not the only way to feel feminine on Valentine"s Day

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TV makeover shows and glossy magazines can leave women feeling guilty for not wearing “sexy” lingerie – especially on Valentine’s Day.But in fact, many different types of underwear could make them feel feminine, according to an expert on underwear consumption.Dr Christiana Tsaousi, a lecturer in marketing and consumption at the University of Leicester’s School of Management, believes underwear choices are hugely affected by personal taste influenced by social background, professional status and upbringing, and why every woman’s underwear needs are individual.Her research on the subject is published today by SAGE in the Journal of Consumer Culture.The ‘shaping’ underwear, for example, prescribed by reality TV shows, such as How To Look Good Naked and 10 Years Younger, is an unhelpful way of thinking about how women should choose what they wear, Dr Tsaousi has concluded.”On Valentine’s Day, some women may feel the only way to feel feminine is to wear the “sexy” underwear promoted by the media in general. But this is really not the case.”“Reality makeover shows and media in general have one purpose – to make women look feminine in line with western ideals,” she said.“They present femininity as this thing where you feel nice about yourself because you have a body that needs to be expressed. Having that as an aim, participants on the shows are given underwear that’s going to mould the body in a certain way.”But Dr Tsaousi, who has conducted extensive research into the consumption of underwear, says that women think very carefully about choosing the right underwear for the right situation – and that comfort is often as important as “sexiness”.“Women learn to choose underwear for the right situation. In an ideal world, it would be good if reality shows acknowledge that women can feel feminine by wearing different underwear.“Some women don’t like these shows because they always show a specific type of femininity, which is not the reality in most cases. They can make you feel guilty about the way you look and the way you feel about your body if you aren’t wearing underwear considered sexy.“When partners are looking to buy underwear as Valentine’s gifts for their wives or girlfriends, they should choose underwear which will fit their partners well and will make them feel comfortable – rather than the stereotypical tiny, uncomfortable types. This will ultimately lead to them feeling nice about themselves.”In her new paper for the Journal of Consumer Culture, Dr Tsaousi interviewed women from a wide range of groups and backgrounds, including university lecturers, young mums, and female rugby players. She looked at the influence of women’s upbringing, profession, age, and social status on their underwear choices.She found that some groups such as the young rugby girls favoured “cute” underwear while for others such as academics something that supports their professional dress was the main priority.“The paper indicates that women’s choices in underwear are determined by factors such as our ways of thinking, up-bringing, taste and status in society,” Dr Tsaousi said. “The paper also suggests that women make similar judgements about their underwear as they would their outerwear.”For many women another big influence on their taste in underwear is their mother.“We can’t forget that the mother normally buys the first bra for her daughter. It is the first act of being feminine, and introduces girls to the idea that they are becoming a woman,” Dr Tsaousi said.Dr Tsaousi added that the study of the consumption of underwear is an area which has not been explored in detail by academics – but is very important to the market.“Obviously women’s outer dress is visible so it is under scrutiny by others. Underwear on the other hand is hidden but people make similar judgements.“Other forms of dress have been widely discussed in consumption studies, but underwear is an area that hasn’t been fully researched. …


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#Agriculture, #Body, #Cancer, #Glossy, #Health, #Journal, #King, #Market, #Pregnancy, #Sexy, #Valentine, #Women