Biology

Peer Mentors Support New Biology Majors

dreessen — Thu, 01 May 2025 16:31:49 +0000

Peer Mentors Support New Biology Majors dreessen Thu, 05/01/2025 - 12:31

Meet Students You Help When You Pay It Forward

dreessen — Wed, 26 Mar 2025 13:55:33 +0000

Meet Students You Help When You Pay It Forward dreessen Wed, 03/26/2025 - 09:55

Heather Carrera

lamontagne — Thu, 20 Mar 2025 13:41:40 +0000

Heather Carrera lamontagne Thu, 03/20/2025 - 09:41

Small Wonders of the Water World

dreessen — Wed, 12 Mar 2025 19:09:56 +0000

Small Wonders of the Water World dreessen Wed, 03/12/2025 - 15:09

A Q&A with Sophomore Sarah Karimi

patenaude — Sat, 08 Mar 2025 08:06:23 +0000

A Q&A with Sophomore Sarah Karimi patenaude Sat, 03/08/2025 - 03:06

A Q&A with Senior Kaden Wheeler '25

patenaude — Thu, 20 Feb 2025 12:58:41 +0000

A Q&A with Senior Kaden Wheeler '25 patenaude Thu, 02/20/2025 - 07:58

Swimming Kinematics of Deep-sea Fishes

patenaude — Fri, 31 Jan 2025 15:10:12 +0000

Swimming Kinematics of Deep-sea Fishes

Friday, January 31, 2025

patenaude Fri, 01/31/2025 - 10:10

Cusk Eel (Image courtesy of NOAA Ocean Exploration)

Mackenzie Gerringer

Summary

In this study, �鶹��ý�Ŷ� students have characterized how fishes swim across habitat depths to 20,000 ft, finding that deep-sea fishes swim consistently slowly, likely due to cold temperatures in the deep sea.

Abstract

Although the deep oceans represent Earth's largest habitat, the challenges of studying deep-sea organisms in situ have limited our understanding of adaptation, ecology, and behaviour in these important ecosystems. One fundamental trait of fishes that remains largely unexplored in the deep ocean is swimming, a vital process for movement, migration, and dispersal in marine habitats. Deep-sea conditions such as temperature, pressure, and food availability could each impact the speed and efficiency of swimming in fishes. To investigate swimming kinematics of fishes with increasing depth, we analysed in situ video of bony fishes across a 6000-m depth gradient. We compared open-source videos of fishes from National Oceanic and Atmospheric Administration (NOAA) Ocean Exploration with tank-based recordings of shallow-water relatives from Puget Sound, Washington, USA to understand how both habitat depth and phylogeny influence swimming in fishes. We analysed kinematics in four dominant demersal fish groups, the orders Anguilliformes, Gadiformes, Ophidiiformes, and Perciformes. Deep-sea fishes swam consistently slowly. Swimming kinematics varied across temperature, oxygen, body elongation, and depth. These results suggest that swimming kinematics do not change linearly with increasing habitat depth in fishes and that the impacts of deep-sea conditions such as low temperatures, high pressures, and low nutrient availability on swimming behaviour need to be considered independently of one another. These findings provide insight into the evolution of fish form and function in the deep ocean.

Primary research questions

How have fishes evolved to swim in the deep ocean?
How does swimming in deep-sea fishes compare to swimming in their shallower-living relatives?

What was known?

Our research builds on anecdotal observations of deep-sea fishes swimming slowly and a few published measurements of swimming speeds in deep-sea species.

What or how does your research add to the field or topic?

This is the first study to investigate swimming in deep-sea fishes across habitat depth within taxonomic orders, allowing us to compare the swimming patterns of closely related species that live at different depths. In this study, deep-sea fishes swam consistently slowly, rather than decreasing swimming speed as depth increased, suggesting that temperature, rather than pressure is likely driving the slow swimming behavior of deep-sea fishes.

Implications for research

These findings provide new insights into how deep-sea conditions drive evolution.

Notable information

This study features four �鶹��ý�Ŷ� alumni from the Department of Biology, including co-lead authors Brett Woodworth '22 and Jessica Palmeri '21.

Brett Woodworth '22, Jessica Palmeri '21, Patrick Flannery '21, and Lydia Fregosi '21 (�鶹��ý�Ŷ�); Cassandra Donatelli (Chapman University).

Woodworth, B., Palmeri, J., Flannery, P., Fregosi, L., Donatelli, C., & Gerringer, M. E. (2024). Swimming kinematics of deep-sea fishes. Journal of Fish Biology, 1–18.

Journal of Fish Biology

The Trypanosoma brucei tRNA methylome

patenaude — Wed, 18 Dec 2024 18:12:24 +0000

The Trypanosoma brucei tRNA methylome

Wednesday, December 18, 2024

patenaude Wed, 12/18/2024 - 13:12

Professor Kevin Militello (�鶹��ý�Ŷ�/Keith Walters '11)

Kevin Militello

Summary:

A map of the positions of 5-methylcytosines in tRNA was made for Trypanosoma brucei, the causative agent of African Sleeping Sickness.

Abstract:

The Trypanosoma brucei procyclic form and bloodstream form tRNA methylome is reported as revealed by small RNA bisulfite sequencing. 5-methylcytosines were identified at six unique positions with 54 total 5-methylcytosines revealed. The main hot spot for 5-methylcytosine in tRNA is the junction between the variable region and the T-arm.

Primary research questions:

1. What are the positions of 5-methylcytosines in Trypanosoma brucei tRNA?
2. Do the 5-methylcytosines positions or levels differ throughout the life cycle of the organism?
3. How do the 5-methylcyotsine positions in Trypanosoma brucei compare to different organisms?

What was known?

At the start of the project, it was known from our past research that T. brucei RNA contains 5-methylcyotsine, but the RNA types, positions, and life cycle regulation was not characterized.

What the research adds to the discussion:

The research indicates that RNAs contain epigenetic modifications (in addition to DNA), and sets up numerous questions on the function of RNA modifications.

Novel methodology:

Sodium bisulfite sequencing of RNA was utilized to find the positions of 5-methylcytosines in RNA.

Implications for society:

It is possible that the enzymes that synthesize 5-methylcytosines represent targets for new drug design to fight infectious disease.

Implications for future research:

We plan to identify the enzymes responsible for 5-methylcytosine in Trypanosoma brucei.

Funding source:

National Institutes of Health grant 1R15AI133428-01

Militello KT. The Trypanosoma brucei tRNA methylome. Microbiol Resour Announc 0:e00579-24. https://doi.org/10.1128/mra.00579-24

Microbial Resource Announcements (2024)

Meet Students You Help When You Pay It Forward

dreessen — Mon, 16 Dec 2024 15:38:07 +0000

Meet Students You Help When You Pay It Forward dreessen Mon, 12/16/2024 - 10:38

Research Shows Growing Evidence of Deep Sea Trash

patenaude — Fri, 29 Nov 2024 17:59:10 +0000

Research Shows Growing Evidence of Deep Sea Trash patenaude Fri, 11/29/2024 - 12:59