Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records

Do you work with or study prokaryotic proteins? As previously announced, we’ve been adding Gene Ontology (GO) terms to RefSeq prokaryotic protein sequence records (example below) to standardize the language when describing the functions of genes and their products. Over 100 million RefSeq proteins from prokaryotes now have at least one GO Term, a 55% … Continue reading Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records

Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records

Do you work with or study prokaryotic proteins? As previously announced, we’ve been adding Gene Ontology (GO) terms to RefSeq prokaryotic protein sequence records (example below) to standardize the language when describing the functions of genes and their products. Over 100 million RefSeq proteins from prokaryotes now have at least one GO Term, a 55% … Continue reading Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records

Conserved Domain Database version 3.20 is available!

A new version of the Conserved Domain Database (CDD) is now available. Version 3.20 contains 1,614 new or updated NCBI/CDD-curated domains and now mirrors Pfam version 34 as well as new models from the NCBIfam collection. Fine-grained classifications of the [(+)ssRNA] virus RNA-dependent RNA polymerase catalytic domain, RING-finger/U-box, dimerization/docking domains of the cAMP-dependent protein kinase … Continue reading Conserved Domain Database version 3.20 is available!

Looking for falsified images in Alzheimer’s study

Charles Piller, for Science, highlights the work of Matthew Schrag, who uses image analysis to look for falsified data, recently scrutinizing a link between a protein and Alzheimer’s:

“So much in our field is not reproducible, so it’s a huge advantage to understand when data streams might not be reliable,” Schrag says. “Some of that’s going to happen reproducing data on the bench. But if it can happen in simpler, faster ways—such as image analysis—it should.” Eventually Schrag ran across the seminal Nature paper, the basis for many others. It, too, seemed to contain multiple doctored images.

Science asked two independent image analysts—Bik and Jana Christopher—to review Schrag’s findings about that paper and others by Lesné. They say some supposed manipulation might be digital artifacts that can occur inadvertently during image processing, a possibility Schrag concedes. But Bik found his conclusions compelling and sound. Christopher concurred about the many duplicated images and some markings suggesting cut-and-pasted Western blots flagged by Schrag. She also identified additional dubious blots and backgrounds he had missed.

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Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

Come visit NCBI at the Bioinformatics Open Science Conference (BOSC), part of the Intelligent Systems for Molecular Biology Conference (ISMB), July 13-16, taking place both in person in Madison, Wisconsin and virtually! We’ll be presenting talks and posters on the latest updates to the NCBI Datasets, BLAST, and Protein resources. You can also join us at … Continue reading Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022

The post Save the Date: NCBI at the Bioinformatics Open Science Conference (BOSC), July 2022 appeared first on NCBI Insights.

Creating a Nutritious Emergency Food Supply

Nutrition Facts label

March is National Nutrition Month.

There are several things to think about when picking food to include in your emergency food supplies. They include:

  • Shelf life. Shop for nonperishable items
  • Foods that don’t require cooking, water, or special preparation are best.
  • Does your family have food allergies or other special dietary needs?
  • How much do you need to keep your family fed? Where will you store it?

Often less attention is paid to the nutritional facts of the foods in our emergency kits. But taking care of your body is an important part of self-care during an emergency. One way to do that is to try to eat healthier foods.

Here are a few tips to help you build a nutritious emergency food supply.

Improve Your Food Label Literacy

Knowing how to read food labels is a practical skill that you can use to make decisions about what goes in your emergency food supply.An annotated example of a Nutrition Facts label.

Nutrition Facts labels include information on serving size, calories, and nutrients that can help you make healthier food choices.(1)

Because you can’t know how an emergency will affect your every day, you may want to stock your food supply with more calories than you normally eat. A day spent cleaning up after a disaster expends more calories than one spent sheltering in place.

When using food labels to help make healthier choices consider the serving size, especially how many servings there are in the food package. The number of servings you eat determines the number of calories you’re eating. Eating too many calories per day is linked to overweight and obesity.

Shop Smart

When shopping for food, imagine having to rely on your emergency food supply and emergency water supply. How will you meet your family’s nutritional needs on a limited supply of water and without access to grocery stores and restaurants? Here are some things to think about when buying for your emergency food supply.

Include Fruits and Vegetables

Canned and shelf-stable fruits and vegetables can be a nutritious addition to your emergency food supply. Look for low and no sodium and no-sugar-added options. Also, consider dried fruit and nuts.

Look for Lower Sodium Foods

Sodium (salt) helps to preserve some foods, especially shelf-stable canned items. Salty food can increase your thirst, which could cause you to drink more water than you planned when creating an emergency water supply.

You should store at least 1 gallon of water per person per day for 3 days for drinking and sanitation. Try to store a 2-week supply of water, if possible.

Most of the sodium you eat is added to packaged foods before you purchase them. This makes reading food labels and choosing lower sodium foods even more important.(2)

Different brands of the same foods may have different sodium levels. For example, sodium in chicken noodle soup can vary by as much as 840 mg per serving for different brands. Look for brands that advertise low or reduced sodium. Compare the nutrition facts panels of different brands to choose the lowest sodium option.(2)

Include Protein

Protein is a critical part of our diet. Everyone needs a minimum amount of protein every day, even during an emergency.

Protein also gives you a feeling of fullness. Feeling full can help keep you from eating other foods in your emergency supply and make your emergency food supply last longer.(3)

Protein-rich foods include:

  • canned or pouched fish,
  • canned poultry,
  • beans and legumes,
  • nuts
  • low-fat or non-fat dairy products packaged in shelf-stable packaging. You can usually find these products in the cereal aisle at the grocery store.

Things like canned or packaged tuna, salmon, or chicken; protein bars, nut butters (presuming no one has an allergy), and some non-dairy milk alternatives are good choices for your emergency food supply.

If buying dairy or non-dairy beverages, look for products that are UHT, or Ultra High-Temperature Pasteurization (also referred to as Ultra Pasteurization or UP). These are shelf-stable and do not require refrigeration for safe storage.

If buying canned proteins, look for labels that say canned in water, low sodium, or no salt added.

Avoid Added Sugars

Added sugars include sucrose, dextrose, table sugar, syrups, honey, and sugars from concentrated fruit or vegetable juices.(4)

The leading sources of added sugars in the US diet are sugar-sweetened beverages, such as regular soda (not sugar-free), fruit drinks, and sports drinks, and foods like cookies and cakes.(4)

One way to avoid added sugars in your emergency food supply is to choose foods with little to no added sugar. Examples include fruit canned in its juice or water.

Help Others Create a More Nutritious Food Supply

People get most of their food for an emergency food supply from food retail venues, such as grocery and corner stores, and food pantries. Having healthier food available and making it affordable in places like these empowers people to make healthier food choices every day and when preparing for emergencies.(5)

When nutritious foods are not available, people may settle for foods that are higher in calories and lower in nutritional value.(5)

The whole community can work together to improve access to healthier food in several ways. They include:

  • connecting people to healthier foods by addressing transportation gaps in communities.
  • increasing nutritious food offerings in food service venues
  • bringing partners together to link local food hubs to organizations that sell or serve food in low-income communities.

Learn more ways government, communities, businesses, nonprofit groups, and others can work to improve access to healthier food.

Resources

References

  1. https://www.fda.gov/food/food-labeling-nutrition/changes-nutrition-facts-label
  2. https://www.cdc.gov/salt/index.htm
  3. https://www.health.harvard.edu/blog/extra-protein-is-a-decent-dietary-choice-but-dont-overdo-it-201305016145
  4. https://www.cdc.gov/nutrition/data-statistics/added-sugars.html
  5. https://www.cdc.gov/nutrition/healthy-food-environments/index.html

Thanks in advance for your questions and comments on this Public Health Matters post. Please note that CDC does not give personal medical advice. If you are concerned you have a disease or condition, talk to your doctor.

Have a question for CDC? CDC-INFO (http://www.cdc.gov/cdc-info/index.html) offers live agents by phone and email to help you find the latest, reliable, and science-based health information on more than 750 health topics.

NCBI will assign 64-bit numeric GIs by November 15th. Update affected software!

As announced  last month, NCBI will begin assigning larger (64-bit) numeric ‘GIs’ to the remaining sequence types that still receive these identifiers. This change is expected as soon as Nov. 15th, 2021 but could occur earlier if data submission volumes are unexpectedly high. This is a reminder that all organizations and developers using our products should review software for any remaining … Continue reading NCBI will assign 64-bit numeric GIs by November 15th. Update affected software!

Vertebrate Genome Project genome assemblies annotated by NCBI

NCBI is an active partner of the Vertebrate Genomes Project (VGP), who recently published a series of papers on the initial results of their efforts to sequence all 70,000 vertebrate species.  See the VGP press release  for more details. To date, this project has submitted over 130 diploid chromosome-level assemblies to NCBI’s GenBank  and the … Continue reading Vertebrate Genome Project genome assemblies annotated by NCBI

Prokaryotic representative genomes updated — now over 13 thousand assemblies!

We have updated the bacterial and archaeal representative genome collection!  The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020.  We’ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and … Continue reading Prokaryotic representative genomes updated — now over 13 thousand assemblies!

The Protein Family Model resource is now available!

The new Protein Family Model resource  (Figure 1) provides a way for you to search across the evidence used by the NCBI annotation pipelines to name and classify proteins. You can find protein families by gene symbol, protein function, and many other terms. You have access to related proteins in the family and publications describing … Continue reading The Protein Family Model resource is now available!