-: 360* Photo: Downloading micro climate data from weather monitors at a granite outcrop in Pickens County, SC :-
2020, June ~ Finishing Manuscripts and Bioinformatics this month. Lots to do.
2020, May ~ Hired as an Assistant Professor of Biology at Anderson University, SC for 2020 - 2021!
2020, April ~ Bioinformatics and teaching remotely going hand in hand.
2020, March ~ CoVid y'all, all lab work on hold :(
2020, February ~ Breaking into the rhythm of juggling a PhD and teaching. Things are interesting.
2020, January ~ hired on as a visiting professor at Anderson University, SC. Excited to teach botany again and intro sciences! Working on bioinformatics and a few manuscripts
2019, December ~ running a final MiSeq run for all 96 samples spanning the southern Appalachians. Started preliminary bioinformatics using Stacks and traditional pipeline.
2019, November ~ more gels, and more gels, and more
2019, October ~ oh wow, we are doing alot of gels this month and extractions. All my library prep is perfect with great results.
2019, September ~ "Passed" my oral comps and have some great preliminary data on the landscape genetics of Micranthes petiolaris. Some interesting results from Structure and Clumpp already, but final sequencing of 96 samples will confirm these shallow results.
2019, August ~ Growth chamber experiments came to a close - alot of phenological data. Also able to to troubleshoot the MiSeq run and now we have lots of data! All of my previously failed seqeunces were rectified with my troubleshooting, so I'm exstatic.
2019, July ~ Sequencing had some issues demultiplexing. I'm frustrated but reviewing the data to troubleshoot.
2019, June ~ Finished my 2nd 2bRad Library and will be ready for sequencing on the MiSeq platform in July. Growth chamber experiment is almost complete.
2019, May ~ Teaching job at a small liberal arts college with research opportunities or a Post Doc? It's time to start looking for opportunities in this last year of research!
2019, April ~ Exciting news on our genome size work using Flow Cytometry. We now have the results of genome sizes for 8 different Saxifragales and a perfected protocol for the BD Accuri 6 FC equipment.
2019, March ~ 2nd run on the MiSeq was successful but not so. All the low elevation samples and 2 of the high elevation tanked near 45 bases, we may have tried to sequence too many cycles when we only needed about 40. Will confer with Illumina.
2019, February ~ planning to run 10 samples on the MiSeq using a v3 150 cycle kit. Going for a spike in of 2% PhiX at 8pmole library concentration. Sanger sequencing of the constructs looks perfect, which is encouraging.
2019, January ~ New semester and back to the very beginning. Becoming a pro at this.
2018, December ~ the month of MiSeq sequencing, and failure! Something went wrong.
2018, November ~ A month of PCR failures, then on the 29th, success! too much digested gDNA seems to inhibit PCR. Serial dilutions of digests are needed to determine optimal amount of digest product for amplification.
2018, October ~ Trying out some new gDNA digest protocols, to see if they are more productive.
2018, September ~ Seeds have dried out and we are now storing them in packets for stratification and growth chamber plantings. Amplification for rad-seq is under way.
2018, August ~ Mounted pressed samples form sites and interred in CLEMS herbarium. Test digests are going well.
2018, July ~ Amplified some genes from all the sites I sampled from. I will have a phylogeny soon that breaks out this population into demes.
2018, June ~ Still collecting regional Saxifragaceae for pilot study on genome sizes. gDNA digests going well.
2018, May ~ Collecting many new Saxifragaceae from the wild to propagate seeds for genomics work. Right now, I'm a Greenhouse King with little brown bags of seeds drying everywhere.
2018, April ~ Punching through extractions for our first digestion utilizing the 2b_Rad method. Updates soon.
2018, March ~ Using a modified Mericon extraction method (Qiagen DNeasy Mericon Kit) I was able to increase my extraction yields up to 8x. That's awesome!
2018, February ~ Interesting paper comparing a Food based DNA extraction kit with other methods (https://doi.org/10.1186/s13007-016-0152-4). Will try this soon.
2018, January ~ A new semester. Teaching load seems to be heavy but we have some new help in the lab.
2017, December ~ Merry Christmas everyone!
2017, November ~ Prepping for some genomic extractions and testing some new high yield protocols.
2017, October ~ Finished some of the highest elevation collections: Roan Mountain, TN, Grandfathers Mountain, NC.
2017, September ~ field collections for vouchers are fruiting in the greenhouse. I will be collecting seeds for future studies.
2017, August ~ Submitted the taxonomic treatment for our new species. Title: A NEW, LOW-ELEVATION APPALACHIAN SAXIFRAGE (MICRANTHES) FROM SOUTH CAROLINA. Reviewers be kind... The Eclipse falls upon us and will be exciting. And school starts back with many new responsibilities.
2017, July ~ Extractions have begun and we nailed down a final protocol for determining genome size in the Saxifrages! Looking forward to sending out a Methods ms soon.
2017, June ~ 8 high elevation mountain ranges in 2 weeks! Close to 500 samples. We also began genomics work, processing standards with our high elevation Micranthes, until the -80*C freezer broke :( check the blog for pics, or Instagram @laaryjc
2017, May ~ Lots of field work and cataloging plants this month. I have hiked so many cliffs and coves, and kayaked a few whitewaters, within GA, SC, and NC, looking for Saxifragales. 105 specimens so far. 4 genera growing in the greenhouse for Genome sizes. Fieldwork to be completed mid June, then we begin extractions and digestions in the lab. 2bRADSeq here we come!
2017, April ~ Yep, I did it. I applied for a grant to attend the 2018 NSF Antarctic Biology Course. Exciting! Check out the course here: https://www.usfca.edu/
2017, March ~ All permits are in! New rapid extraction protocol tested! Primers all functional! Now all we need are the plants. Look out Appalachians 😀
2017, February ~ Most permits are in. Excited about all of the plant populations and places we will visit throughout the Appalachians! Over 17 sites will need to be hiked, inventoried, sampled, and enjoyed.
2017, January ~ New nuclear isolation protocol unreported for our family of plants works! Looking forward to reporting on seven Southern Appalachian endemics, and maybe anything else we can get our hands on.
2016. December ~ Beginning some exciting work on Genome size of flora within the Appalachians!
2016, November ~ Draft Dissertation Research Proposal submitted!
2016, January ~ New study plots established for floral characteristics study within the Blue Ridge Escarpment. Looking forward to recording phenology as well and starting some much needed genomic extractions.
2015, December ~ Funding acquired! We will continue our research within the Saxifragaceae and expand to two more taxa located throughout the Blue Ridge Escarpment, investigating allele retention rates among isolated conspecifics and community associated taxa.
2015, November ~ Honored to be working with some great folk on my PhD research:
2015, October ~ Excited about a grant funding opportunity of $10,000 for continued genomic work on our species novum and its sister taxa! A few
meetings away from doing more great things in the lab and field.
2015, September ~ Microsatellites arrived for the Saxifragaceae. Will test these at the end of month on regional extractions.
2015, August ~ LiCor studies on high elevation populations just completed. A lot of data gathered on over 30 plants. Excited to see what they're doing in all that cloud cover.
2015, July ~ Interviewed for Adjunct position at Anderson University. Offered position to teach 2 classes during interview; Wow!
2015, June ~ Defended my thesis and passed the exam! Onto the PhD.
2105, May ~ LiCor studies completed at our low elevation site. Over 50 samples. Excited for this early start on my PhD research.
2015, April ~ Thesis done and submitted for review.
2015, February ~ Invited as a guest lecturer to the Warren Wilson College Shared Genetics Laboratory. NC. I presented my research, “Phenotypic differences of a Blue Ridge Escarpment endemic at variable elevations."
2014, November ~ Wade T Batson Grant Recipient for Field Botany Research - $1000.00
Another great opportunity to further the research and delve into the gene-flow of our study.
2014, July ~ Received my official certification as a Taxonomist with the Society for Freshwater Scientists.
2014, July ~ Highlands Biological Station, Summer Studies Invitation & Funding Awarded
Looking forward to a month of field work studying the conservation genetics of salamanders and macro-invertebrate taxonomy.
2014, April ~ Presented a poster at the 75th annual ASB conference, 75th Annual Meeting Program of the Association of Southeastern Biologists, "Incipient Speciation in Hydatica Necker", research colleagues include Patrick McMillan of Clemson University, SC, and Kathy Mathews of Western Carolina University, NC. Great group of researchers.
2020, May ~ Hired as an Assistant Professor of Biology at Anderson University, SC for 2020 - 2021!
2020, April ~ Bioinformatics and teaching remotely going hand in hand.
2020, March ~ CoVid y'all, all lab work on hold :(
2020, February ~ Breaking into the rhythm of juggling a PhD and teaching. Things are interesting.
2020, January ~ hired on as a visiting professor at Anderson University, SC. Excited to teach botany again and intro sciences! Working on bioinformatics and a few manuscripts
2019, December ~ running a final MiSeq run for all 96 samples spanning the southern Appalachians. Started preliminary bioinformatics using Stacks and traditional pipeline.
2019, November ~ more gels, and more gels, and more
2019, October ~ oh wow, we are doing alot of gels this month and extractions. All my library prep is perfect with great results.
2019, September ~ "Passed" my oral comps and have some great preliminary data on the landscape genetics of Micranthes petiolaris. Some interesting results from Structure and Clumpp already, but final sequencing of 96 samples will confirm these shallow results.
2019, August ~ Growth chamber experiments came to a close - alot of phenological data. Also able to to troubleshoot the MiSeq run and now we have lots of data! All of my previously failed seqeunces were rectified with my troubleshooting, so I'm exstatic.
2019, July ~ Sequencing had some issues demultiplexing. I'm frustrated but reviewing the data to troubleshoot.
2019, June ~ Finished my 2nd 2bRad Library and will be ready for sequencing on the MiSeq platform in July. Growth chamber experiment is almost complete.
2019, May ~ Teaching job at a small liberal arts college with research opportunities or a Post Doc? It's time to start looking for opportunities in this last year of research!
2019, April ~ Exciting news on our genome size work using Flow Cytometry. We now have the results of genome sizes for 8 different Saxifragales and a perfected protocol for the BD Accuri 6 FC equipment.
2019, March ~ 2nd run on the MiSeq was successful but not so. All the low elevation samples and 2 of the high elevation tanked near 45 bases, we may have tried to sequence too many cycles when we only needed about 40. Will confer with Illumina.
2019, February ~ planning to run 10 samples on the MiSeq using a v3 150 cycle kit. Going for a spike in of 2% PhiX at 8pmole library concentration. Sanger sequencing of the constructs looks perfect, which is encouraging.
2019, January ~ New semester and back to the very beginning. Becoming a pro at this.
2018, December ~ the month of MiSeq sequencing, and failure! Something went wrong.
2018, November ~ A month of PCR failures, then on the 29th, success! too much digested gDNA seems to inhibit PCR. Serial dilutions of digests are needed to determine optimal amount of digest product for amplification.
2018, October ~ Trying out some new gDNA digest protocols, to see if they are more productive.
2018, September ~ Seeds have dried out and we are now storing them in packets for stratification and growth chamber plantings. Amplification for rad-seq is under way.
2018, August ~ Mounted pressed samples form sites and interred in CLEMS herbarium. Test digests are going well.
2018, July ~ Amplified some genes from all the sites I sampled from. I will have a phylogeny soon that breaks out this population into demes.
2018, June ~ Still collecting regional Saxifragaceae for pilot study on genome sizes. gDNA digests going well.
2018, May ~ Collecting many new Saxifragaceae from the wild to propagate seeds for genomics work. Right now, I'm a Greenhouse King with little brown bags of seeds drying everywhere.
2018, April ~ Punching through extractions for our first digestion utilizing the 2b_Rad method. Updates soon.
2018, March ~ Using a modified Mericon extraction method (Qiagen DNeasy Mericon Kit) I was able to increase my extraction yields up to 8x. That's awesome!
2018, February ~ Interesting paper comparing a Food based DNA extraction kit with other methods (https://doi.org/10.1186/s13007-016-0152-4). Will try this soon.
2018, January ~ A new semester. Teaching load seems to be heavy but we have some new help in the lab.
2017, December ~ Merry Christmas everyone!
2017, November ~ Prepping for some genomic extractions and testing some new high yield protocols.
2017, October ~ Finished some of the highest elevation collections: Roan Mountain, TN, Grandfathers Mountain, NC.
2017, September ~ field collections for vouchers are fruiting in the greenhouse. I will be collecting seeds for future studies.
2017, August ~ Submitted the taxonomic treatment for our new species. Title: A NEW, LOW-ELEVATION APPALACHIAN SAXIFRAGE (MICRANTHES) FROM SOUTH CAROLINA. Reviewers be kind... The Eclipse falls upon us and will be exciting. And school starts back with many new responsibilities.
2017, July ~ Extractions have begun and we nailed down a final protocol for determining genome size in the Saxifrages! Looking forward to sending out a Methods ms soon.
2017, June ~ 8 high elevation mountain ranges in 2 weeks! Close to 500 samples. We also began genomics work, processing standards with our high elevation Micranthes, until the -80*C freezer broke :( check the blog for pics, or Instagram @laaryjc
2017, May ~ Lots of field work and cataloging plants this month. I have hiked so many cliffs and coves, and kayaked a few whitewaters, within GA, SC, and NC, looking for Saxifragales. 105 specimens so far. 4 genera growing in the greenhouse for Genome sizes. Fieldwork to be completed mid June, then we begin extractions and digestions in the lab. 2bRADSeq here we come!
2017, April ~ Yep, I did it. I applied for a grant to attend the 2018 NSF Antarctic Biology Course. Exciting! Check out the course here: https://www.usfca.edu/
2017, March ~ All permits are in! New rapid extraction protocol tested! Primers all functional! Now all we need are the plants. Look out Appalachians 😀
2017, February ~ Most permits are in. Excited about all of the plant populations and places we will visit throughout the Appalachians! Over 17 sites will need to be hiked, inventoried, sampled, and enjoyed.
2017, January ~ New nuclear isolation protocol unreported for our family of plants works! Looking forward to reporting on seven Southern Appalachian endemics, and maybe anything else we can get our hands on.
2016. December ~ Beginning some exciting work on Genome size of flora within the Appalachians!
2016, November ~ Draft Dissertation Research Proposal submitted!
2016, January ~ New study plots established for floral characteristics study within the Blue Ridge Escarpment. Looking forward to recording phenology as well and starting some much needed genomic extractions.
2015, December ~ Funding acquired! We will continue our research within the Saxifragaceae and expand to two more taxa located throughout the Blue Ridge Escarpment, investigating allele retention rates among isolated conspecifics and community associated taxa.
2015, November ~ Honored to be working with some great folk on my PhD research:
- Dr. Vincent Richards (http://www.vprichards-lab.com/)
- Dr. Christina Wells (http://www.clemson.edu/cafls/departments/biosci/faculty_staff/wells_c.html)
- Dr. Patrick McMillan (http://www.clemson.edu/cafls/safes/faculty_staff/mcmillan.html)
- Dr. Antonio Baeza (http://baezaantonio.wix.com/antoniobaeza)
- Dr. Alisa Hove (https://www.warren-wilson.edu/academics/biology)
2015, October ~ Excited about a grant funding opportunity of $10,000 for continued genomic work on our species novum and its sister taxa! A few
meetings away from doing more great things in the lab and field.
2015, September ~ Microsatellites arrived for the Saxifragaceae. Will test these at the end of month on regional extractions.
2015, August ~ LiCor studies on high elevation populations just completed. A lot of data gathered on over 30 plants. Excited to see what they're doing in all that cloud cover.
2015, July ~ Interviewed for Adjunct position at Anderson University. Offered position to teach 2 classes during interview; Wow!
2015, June ~ Defended my thesis and passed the exam! Onto the PhD.
2105, May ~ LiCor studies completed at our low elevation site. Over 50 samples. Excited for this early start on my PhD research.
2015, April ~ Thesis done and submitted for review.
2015, February ~ Invited as a guest lecturer to the Warren Wilson College Shared Genetics Laboratory. NC. I presented my research, “Phenotypic differences of a Blue Ridge Escarpment endemic at variable elevations."
2014, November ~ Wade T Batson Grant Recipient for Field Botany Research - $1000.00
Another great opportunity to further the research and delve into the gene-flow of our study.
2014, July ~ Received my official certification as a Taxonomist with the Society for Freshwater Scientists.
2014, July ~ Highlands Biological Station, Summer Studies Invitation & Funding Awarded
Looking forward to a month of field work studying the conservation genetics of salamanders and macro-invertebrate taxonomy.
2014, April ~ Presented a poster at the 75th annual ASB conference, 75th Annual Meeting Program of the Association of Southeastern Biologists, "Incipient Speciation in Hydatica Necker", research colleagues include Patrick McMillan of Clemson University, SC, and Kathy Mathews of Western Carolina University, NC. Great group of researchers.