Last month the Sackler Insight hosted a contest to find the best science-based art (“sci-art”) at Sackler. All twelve entries were posted to the Sackler Graduate Student Council Instagram account (@SacklerGSC) and the Sackler student Facebook group. The winning contributor will receive a $25 Visa gift card!
The results are in! 174 voters from both Instagram and Facebook weighed in on their favorite pictures. Our lucky first place winner is Mary H. from Microbiology with her photo “An enteroid supernova,” which received 65 votes. Runners-up included Rana A. from PDD with “Making the best of a bad Western” (61 votes) and Rob C. from CMDB with “Monday Blues – Screening One-Bead-One-Compound Peptide Libraries” (39 votes).
Congratulations Mary, and thank you to everyone who participated! You can check out the pictures below:
A neuron filled with red fluorescent protein (RFP) and GFP tagged Farp1, which localizes to spines where connections to other neurons form. Contributed by Andrew C. from Neuroscience.
Heterogeneity of mitochondrial membrane potential in a population of murine chondrocytes (red=greater membrane polarization). Contributed by Judi H. from CMDB
An enteroid supernova. Contributed by Mary H. from Microbiology.
GABAergic inhibitory neurons (parvalbumin+ basket cells, red) in the mouse dentate gyrus, an important structure for learning and memory. Contributed by Matt K. from Neuroscience.
Growth of human luminal (red) and basal (green) mammary epithelial cells in 3D hydrogels. Contributed by Jess E. from CMDB.
Auto-fluorescence from the internal elastic lamina: how scientific aggravation becomes art. Contributed by Jess D-K. from CMDB.
The normal & the pathological – Disorganization in breast tissue architecture during carcinogenesis. Contributed by Nafis H. from CMDB.
There is always light in the darkness. (CD3 (green) and tdTomato (red) as a lineage trace in a mouse lymph node). Contributed by Linus W. from Immunology.
Human mammary epithelial cells pull and twist rat-tail collagen fibers during their formation into a hollow duct-like structure. Contributed by Michael S. from Genetics.
Making the best of a bad western. Contributed by Rana A. from PDD.
Monday Blues – Screening One-Bead-One-Compound Peptide Libraries. Contributed by Rob C. from CMDB.
We frozen few doing our thesis work in the CMDB and genetics programs are always looking for ways to highlight some of the excellent resources we have at our institutes. Last month I had the pleasure of hosting the CMDB first year students and introducing them to the Maine Medical Center Research Institute in Scarborough, Maine. They heard from the faculty here about potential rotation projects, but perhaps more importantly about the larger on-going projects that could become collaborative efforts between Maine and Boston. Here are some pictures of their visit and a link to the updated MMCRI website in case you too are interested in finding out about current MMCRI research.
Left to right CMDB first years Brittany Ahlstedt, Alexander Hu, Alice Meng, and Jackson Fatherree at Portland Head Light at Fort Williams Park.
Left to right CMDB students Alice Meng, Brittany Ahlstedt, Jess Davis-Knowlton, Jackson Fatherree, and Alexander Hu at Duckfat in Portland.
The recent tax reform bill passed in the House caused much uproar in the academic community as it removed the provision in the current tax code that waives the students’ school tuition. This provision, known as qualified-tuition-reduction provision (section 117(d)(5)), allows for the waived tuition to be exempt from taxable income; removal of this provision would therefore add to the tax burden of the students, who are already living marginally with an average income of ~$30,000/year. Sackler students, who currently receive $33,500, would see their taxable income increase by ~$20,000 (annual tuition) which would push them to a higher tax bracket (15% to 25%). It should be noted that this tuition waiver provision does not affects students in their 6th or higher year of study at Sackler as tuition is not charged past the 5th year.
Fortunately, the Senate’s version of the new tax bill retains this provision, for now. It remains to be seen whether the merged version of the bill will keep or remove this provision. In the meantime, graduate students have been organizing nationwide; the Sackler graduate student council organized a call your representatives event last Tuesday. If you haven’t gotten a chance to make your voice heard yet, consider signing onto FASEB’s letter to Congress asking them to protect the waiver provision.
The fight to protect this provision has raised other questions among grad students, particularly, why do universities bill tuition and then waive it? It appears that the waiver is not done in the same manner across all private universities. For example, Cornell University considers its tuition waiver as a qualified scholarship, which is tax exempt and not affected by the removal of the provision in the House bill. But this still allows for the question to be asked as to why universities just don’t charge $0 for tuition or if they can NOT charge it after 5 years, why they can’t do it for the years before. The answer seems to lie with the fact that universities are using the billed tuition as a way to generate revenue, especially in the sciences. This may sound sinister, but the reality is more complex. As scientists & trainees supported mostly by government grants, we are all aware of the overhead & indirect costs that are involved with doing research and that a percentage of every grant awarded to a faculty member at the university is matched by the NIH and given to the university administration. This support is necessary for maintaining a research environment, but it also begs the question of whether taxpayer money should be used to fund administrations of private universities with large endowments, particularly at a time when budgets for scientific endeavors are being slashed. Additionally, given that private universities, which enjoy a non-profit status, are behaving more and more like for-profit institutions, one is left to wonder whose interests are being represented at the administrative level.
The grad student tax debate has also raised the question of the role of graduate students in the workplace. Traditionally, graduate students have been considered as trainees rather than employees and a certain paternalistic relationship exists between faculty/administration & graduate students. However, since the National Labor Relations Board’s decision to recognize graduate students as employees, thus allowing them to unionize, this trainee status is being questioned more and more. Graduate students have faced obstructions from the university administrations when they have tried to unionize, and faculty have been divided on the topic of whether students should unionize (one professor going as far to tell grad students to focus on work rather than wages). Tufts currently has a graduate student union, but the Sackler school doesn’t have one at the moment, reasons for which lie with the content student body and the lack of a teaching requirement as part of the stipend.
It seems that the tax bill requires major revisions, for reasons separate from the grad student tax. This gives us, academics, time to organize around this issue and keep putting pressure on our representatives to protect the tuition waiver for graduate students. This also allows us to have a broader discussion about the roles of graduate students in the workplace, and how universities use funds that they receive from the public through the government funding bodies. Transparency from the administration’s side is likely to win them more supporters among students and faculty alike, rather than a nebulous state of operations.
This database indexes biomedical journal articles and conference abstracts. The database includes thousands of journals not indexed by MEDLINE (PubMed), and is particularly robust in its coverage of pharmaceutical and medical device literature and conferences. Unique indexing, through its Emtree controlled vocabulary, and search features make it easy to retrieve precise results.
Springer Nature Experiments, which I mentioned in my October post, is now available. To access, click the link in the ‘Find Springer Nature Protocols & Methods’ box on the Sackler School Biomedical Sciences Research Guide
Life After Life is a novel about an English woman who lives through the events of the first half of the 20th century again and again, with small, but critical, changes each time, reminiscent of Ray Bradbury’s short story, A Sound of Thunder. A God in Ruins is the companion novel to Life After Life, following the brother of the main character in the first novel through his experiences in World War II to the present day.
To request a book from another Tufts Library:
Search for the book in JumboSearch, which is the default search on the Hirsh Health Sciences Library homepage.
Once you find the book, click the title to view the record for that book. Click the ‘Log in’ link in the yellow box.
Log in with your Tufts username and password.
Once you have logged in, click the ‘Request item’ link.
Choose your pickup location (Hirsh Health Sciences Library) and click ‘Request’. You will be notified via email when the book is ready for you to pick up.
PubMed is just one database from the National Library of Medicine (NLM). The National Center for Biotechnology Information (NCBI), a division of the NLM, maintains several molecular biology databases. These databases link to one another and to PubMed. This month, I’ll describe how to find information about a gene in PubMed and the Gene database.
Which NCBI resource(s) should I use to find information on a gene?
You can start in either PubMed or Gene, a database of known and predicted genes for a several species. Each record is devoted to a single gene and may provide information on nomenclature, chromosomal location, gene products, phenotypes, and interactions, as well as links to literature, sequences, and other NCBI and external databases. Consider a Gene record a gene’s homepage in NCBI.
I’ll begin in PubMed because it is the database with which you are likely most familiar. In the PubMed search box, you can enter either a gene’s name or symbol. To activate the Gene Sensor (see next question), use the official gene symbol, which can be found at genenames.org, the site for the HUGO Gene Nomenclature Committee (HGNC). The HGNC assigns standardized names to human genes.
What is the PubMed Gene Sensor?
Gene Sensor checks the gene symbol that you enter against symbols in the Gene database and, if a match is found, displays links to information about the gene in NCBI databases at the top of your PubMed search results. These links include: the records(s) for the gene in the Gene database; articles on the gene’s function (GeneRIF; see below); and tests in the Genetic Testing Registry.
Choose the link to the gene’s record in the Gene database. The first option will be for the human gene, with links for other species, if available, following.
Gene Sensor results in PubMed
What if my initial PubMed search does not activate the Gene Sensor?
If you do not see the Gene Sensor box at the top of your PubMed results, then you can search the Gene database directly by selecting ‘Gene’ from the drop-down menu next to the search box. Enter a gene name or symbol, species, or disease.
Choose Gene database from drop-down menu
How do I find information once I am in a Gene record?
Use the Table of Contents in the right-hand column of the record to navigate to specific information about the gene. Scroll down to the ‘Related information’ section of the right-hand column for links to information about the gene in other NCBI databases.
Record in Gene database, with Table of Contents in right-hand column
So how does this help me find PubMed articles about a gene?
In the Related information section of a Gene record, you will notice several links to PubMed. Each of these links retrieves a specific set of articles in PubMed:
PubMed: Articles that have been indexed with the Medical Subject Heading (MeSH) of the protein that the gene codes for, combined with the subheading ‘genetics’. For example: ‘Hemochromatosis Protein/genetics’[MeSH].
PubMed (GeneRIF): Articles that focus on the function of a gene. GeneRIFs (reference into function) are identified in three ways: by National Library of Medicine staff; by volunteer collaborators who submit a function, and article(s) describing that function (if you know of, or have authored, an article about a gene’s function, then you can submit a GeneRIF); through reports from HuGE Navigator, a human genome epidemiology knowledge base from the Centers for Disease Control and Prevention. PubMed (GeneRIF) also includes articles that describes a gene’s interactions.
PubMed (OMIM): Articles cited in Online Mendelian Inheritance in Man (OMIM) records. OMIM is a compendium of human genes and phenotypes.
PubMed (nucleotide/PMC): Articles identified from shared sequence and PubMed Central links.
Each set of articles is continuously updated. Use these links to retrieve the set of articles that best describes the type of literature you are seeking.
PubMed links under ‘Related information’ in Gene record
What if I want to find all the literature on a particular gene in PubMed?
If you want to do a comprehensive PubMed search for literature on a gene, then use the Gene record and HGNC (genenames.org) to identify the gene’s current and past names, symbols, and synonyms. Use ‘OR’ to combine these keywords with the MeSH term for the protein that the gene codes for, with the subheading ‘genetics’. Some genes, but not all, genes also have a MeSH term for the gene itself.
For example:
“BRCA1” OR “BRCC1” OR “FANCS” OR “BROVCA1” OR “PPP1R53” OR “breast cancer 1” OR “Genes, BRCA1″[MeSH] OR “BRCA1 Protein/genetics”[MeSH]
You may get a lot of irrelevant results with a comprehensive search because many gene symbols are not unique. Therefore, this search would likely have to be combined with another concept, using ‘AND’.
For example:
(“BRCA1” OR “BRCC1” OR “FANCS” OR “BROVCA1” OR “PPP1R53” OR “breast cancer 1” OR “Genes, BRCA1″[MeSH] OR “BRCA1 Protein/genetics”[MeSH]) AND (“ovarian neoplasms”[MeSH] OR “ovarian neoplasms” OR “ovarian cancer”)
