As we push forward integrating neuroscience resources, literature & data – we are always looking for novel, helpful and exciting neuroscience related content to integrate within the semantically-enhanced NIF system. In fact, if you have a neuroscience resource and would like to register it with NIF, please check out the tutorial for Registering your Resource with NIF.

Scientists, students, administrators..practically everyone is reading multiple large documents per day which requires time, attention and, of course, enough lexical knowledge to fully grasp its meaning. Fortunately, there is YouTube for that downtime (i.e. the latest cat meme). However, there have been a number of new sites dedicated solely to scientific content.

Scivee.tv is a great example.

They allow scientists to upload video summaries of their work – so rather than just read the article, you are able to watch the scientist explain the research and even watch the video with an auto scrolling feature taking you to the relevant part in the article – check out the video here.

the Journal of Visualized Experiments (JOVE) is another great example.

With a special section dedicated to neuroscience, JOVE provide excellent video tutorials for laboratory protocols and methods – one thing, in particular, that is easier to pick up by watching rather than reading.

Lastly, YouTube does in fact have a lot of interesting, neuroscience-related videos – most of them being video presentations from conference proceedings or well-produced interviews with prominent scientists.

In the future, we would like to curate these videos and provide the NIF community to search for and save their favorite neuroscience videos. We will be sure to update the community as these features roll out and as always we love to hear your feedback. If you have any ideas or know of similar science-related video sites, please feel free to contact us by any means or post a comment below!

Inside NIF appears every Wednesday on the NIF Blog. Join us each Wednesday to learn more about what’s happening at NIF, your Neuroscience Information Framework.

The National Center for Biotechnology Information (NCBI) is a national institute under the National Library of Medicine which holds vast amounts of biological data. Entrez is an web portal or federated search engine provided by NCBI to allow scientists to access this information. In this blog post, we will look at NCBI Entrez:Gene, one of the many databases in the Entrez system.

Information in NCBI Entrez: Gene can be easily accessed through NIF by searching for specific gene of  interest. For example,  to learn more about the gene pca, try performing the following search in NIF: “gene: pca”. NCBI Entrez:Gene can be found under Nervous System Level > Gene > EntrezGene: NCBIGene (shown below).

The result displays the Gene Symbol, Synonyms, Type, Description and Organism. Clicking on the gene name will take you to the NCBI Entrez:gene portal with more details about the gene.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

Using a silicon wafer with adhesion proteins, researchers at the University of Pittsburgh have opened a new window to study prolonged neuronal activity – particularly that behind memory formation.

Above is a florescent image of the neuronal network developed at Pitt. It shows individual neurons (blue), adhesive proteins (green) and neuronal connections (red) on the silicon disk that allow for investigation of neuronal communication and activity. Reported in the journal Lab on a Chip, “Ring-shaped neuronal networks: a platform to study persistent activity” describes this pioneering work.

Using embryonic rat hippocampal cells, the researchers were able to excite the neurons using an electrical pulse and investigate the sustained network activity for 12 seconds – a process with a natural duration of around .25 seconds. Therefore, they were able to extensively observe neuronal transmission and prolonged maintenance of the electrical charge.

This will offer neuroscientists a novel way to study the cellular and molecular mechanics of persistent neuronal activity, which is key to understanding memory formation. In the future, they hope to understand the factors at the foundation of neuronal transmission including the genetic and epigenetic factors that influence electrical communication between neurons.

Extending our window of observation from .25 seconds to 12 seconds…now that is dangerous..and for that we thank you!

After the success of Inside NIF: The Cell: An Image Library – mobile phone wallpapers, we have decided once again to comb The Cell: An Image Library for exciting and interesting neuroscience images for your enjoyment and download – this time as desktop wallpapers. To load the full-size image, simply click the image you like.

Check back on the first Wednesday of each month for new neuroscience images gathered from Image sources within the Neuroscience Information Framework!

Image 1: Filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons.

(Authors: Dieter Brandner, Ginger Withers )

Image 2: Interneurons expressing EGFP from the 5HT3 receptor promoter in the dorsal hippocampus colabelled for the CB1 cannabinoid receptor (red) and counterstained with DAPI (blue) to show the cell layers.

(Author: Margaret I. Davis)

Image 3: Hippocampal neurons expressing EGFP from the Nr4a1/Nur77 promoter colabelled with calbindin 28K (red) and stained with DAPI (blue) to show cell layers.

(Author: Margaret I. Davis)

Image 4: Distribution of interneurons expressing EGFP from the 5HT3 receptor promoter colabelled for the CB1 cannabinoid receptor in hippocampal CA1.

(Author: Margaret I. Davis)

Image 5: The CA region of the hippocampus of adult rat, immunostained to reveal dendrites of neurons (red), astroglia (green) and all nuclei (blue).

(Authors: Christopher Wallace, Ginger Withers, Tony Cooke )

Inside NIF appears every Wednesday on the NIF Blog. Join us each Wednesday to learn more about what’s happening at NIF, your Neuroscience Information Framework.

The Cell: An Image Library is a public and easily accessible resource database of images, videos, and animations of cells. It captures a wide range of organisms, cell types, and cellular processes in order to advance research on cellular activity and ultimately improve human health.

Through NIF, The Cell Image Library can be searched by a specific cell, brain region or biological process. For example, a search for an image of the tectum returns results found under Data Type > Images > CellImageLibrary (shown below) or Nervous System Level > Cellular Level > CellImageLibrary.

Here you can find the image file name, subject type, attribution, image description, cellular component and biological process. Clicking on the image will take you to the library’s website (shown below).

So go ahead a give it a try, search NIF for a biological process – synaptic development, or even a cellular component – synapse to find highly annotated, semantically linked images in The Cell: an Image Library.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

In this presentation, Discovery: First Scientifically Confirmed Poisonous Bird, Dr. Jack Dumbacher explains the discovery of the first poisonous birds – the hooded pitohui, native to New Guinea.

Possessing a neurotoxin of the Batrachotoxin family, these birds can rub off a steroid compound that blocks sodium ion channels. This prevents the neuron from returning to polarized resting state, and eventually kills predators or prey by eliminating neurotransmission to the muscles (i.e. heart). It is believed that the birds became poisonous due to their dietary intake of a beetle which contained the barachotoxin, essentially seeping the alkaloid out through their skin. Either way – the first scientifically confirmed poisonous bird?…..now thats dangerous, and for that we thank you hooded pitohui.

There are tens of thousands of different biological pathways and each pathway involves complex sets of protein-protein interactions, small molecules, protein complexes, enzymes, regulators and reactions. These pathways are represented in published papers, databases and scientists heads; however now they can also be found on WikiPathways: an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. WikiPathways is a wiki so it is possible to access and contribute biological pathway information easily.

NIF’s federated search engine searches some information in WikiPathways such as pathway name, gene name, gene symbol, or organism. For example, we can search for Wnt signaling pathway in zebrafish (Wnt proteins are part of basic developmental processes, such as cell-fate specification, cell proliferation and asymmetric cell division) using the search syntax “Zebrafish Wnt signaling pathway”.

Categories returned, as mentioned above, are pathway name, gene symbol, gene name, and organism. Clicking on the pathway name will take the users to WikiPathways page for more details on the pathway.

Information on Wikipathways page includes the current diagram, description, references, download options, version history, and component gene and protein lists.

For more thorough instructions on how to use Wikipathways, please visit NIF’s Wikipathways tutorial.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line at curation@neuinfo.org.

Pictures have taken over painting, mosaics and caricatures have proliferated insidiously so what then can the modern lord or baron do to impress his friends? I introduce you to the very NIFARIOUS: DNA portrait!

DNA portrait gives people an opportunity to frame themselves as the very base code of themselves; the ones and zeros of their personal code; their DNA. It combines latest technologies, DNA sequencing and its visualization, to come up with an aesthetic representation of your genomic make-up. If you are ever accused of a crime, your DNA portrait will be turned right over to the police from your coffee table!

So to get your very own portrait, the company will send you a DNA kit, you swab the inside your mouth for cheek cells and send it back.

The service is pricey, but all of those old money or Nouveau riche may be able to consider this or the space flight vacation.

*Pictures and information are taken from DNA11, a company *

Note, NIF is in no way affiliated with this company, but does think that this is pretty funny.

In previous blog post, we have talked about the importance of C. elegans, or Caenorhabditis elegans, and how its genomic information can be accessed through Wormbase: Genes. In this blog post, we will discuss how we can utilize wormbase to learn more about the anatomy of C. elegans.

Wormbase: Anatomy is an ontology of controlled vocabulary for cellular anatomy. It has short description of an anatomical terms and shows its relationship to other terms in the ontology. Below is a portion of a result returned when gabaergic neuron is searched in the WormBase: Anatomy.

Using NIF, Wormbase: Anatomy can be accessed by searching for specific anatomical terms. For example, if we would like to receive an information on gabaergic neuron like the one above, we can use the search syntax gabaergic neuron. WormBase Anatomy can be found under Nervous System Level -> Cellular Level -> WormBaseAnatomy

Searching in NIF returns anatomical term, its description, expressed genes and affected phenotypes. Clicking on the term will take users to the WormBase: Anatomy page with more detailed information. For more instructions on how to use WormBase Anatomy, please visit WormBase: Anatomy Tutorial.

The NIF Data Spotlight is a weekly blog post highlighting the databases, information, and resources curated by the Neuroscience Information Framework. For comments, questions or concerns feel free to drop us a line atcuration@neuinfo.org.

There is virtually an app for everything these days. Yes, that statement hold true for cancer diagnosis. Using a cell phone and a lunch box- sized machine, a team from Harvard Medical School was able to diagnose cancer outside of a clinic. The technology uses magnetic resonance to measure certain antibody activity within the sample. The result is transmitted to the cell phone and the result is displayed through an app. This will allow many forms of diagnostics to move away from the lab and bring it to the outside world where real time diagnosis is possible.

This technology goes beyond just cancer diagnosis. Using different diagnosis platforms, it is possible to diagnose almost any diseases. In addition, the improvement is quality of camera within the cell phone allows researcher to take a picture of sample and analyze it without the use of microscopes. With further advancement in technology, it might not be impossible to carry out many researches, diagnosis and analysis with just your phone.

The current technology of mobile phone as a research tool certainly has its limits. It is not yet practical nor efficient enough to be widely used among scientists. However, its possibility is without a bound, and has the potential to bring major impact to the world of science. We do not know how this will turn out in the end but its IDEA is definitely NIFARIOUS!