SIO 126 Week 3 Discussion - Monday by Ivan Moreno https://padlet.com/imoreno93/jiiuny712xnmf6hg SIO-126: Week 3 Discussion: review questions from class & section questions en-us 2022-01-20 19:33:17 UTC 2023-01-26 00:53:53 UTC hello@padlet.com primer helps start DNA replication or transcription, probe helps mark/identify a matching nucleotide https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456896378 2023-01-25 23:24:50 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456896378 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897167 Compare the molecular weight to isotopes with their functions —> markers of biological processes ]]> 2023-01-25 23:26:25 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897167 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897196 A primer is a short single stranded nucleic acid that provides a starting point for DNA synthesis and a probe is a single stranded sequence of DNA or RNA that is used to identify the complementary sequence in a sample genome. ]]> 2023-01-25 23:26:30 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897196 Can be used as a marker https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897239 2023-01-25 23:26:34 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897239 A probe is a short strand of DNA that can be labeled to hybridize to a complementary molecule where as a primer is what is used for the synthesis of a new DNA strand https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897562 2023-01-25 23:27:13 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897562 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897566 Primer is already in the DNA sequence and tells it when to start transcription and a probe is introduced to the DNA/RNA to find the matching part (nucleotide-wise)

]]> 2023-01-25 23:27:13 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897566 Not all cells will lyse at the same rate, so some organisms will be over/under represented https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897652 2023-01-25 23:27:24 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897652 identifying transfer of genes between microbes(?) or transfer of bio material https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897678 2023-01-25 23:27:28 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456897678 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898393 They can see how the element is travelling through the food chain]]> 2023-01-25 23:28:54 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898393 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898728 niskin bottle: cylinder used to collect water, will only close when it reaches user specified depth]]> 2023-01-25 23:29:34 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898728 corers https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898848 2023-01-25 23:29:52 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898848 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898873 direct counts

]]> 2023-01-25 23:29:56 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898873 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898890 To make similar environment in a lab setting using Agar or Silicate plate. Some methods include streaking and spreading ]]> 2023-01-25 23:29:57 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898890 can be used to mark certain pathways or functions https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898920 2023-01-25 23:30:01 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456898920 a sedigned PCR primer will only bind to a specific site, so if the PCR primer is off, it wont do PCR https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899062 2023-01-25 23:30:21 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899062 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899287 Flow Cytometry, Direct counts, FISH]]> 2023-01-25 23:30:51 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899287 metatranscriptomic sequencing https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899357 2023-01-25 23:30:59 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899357 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899700 All of the same family have core genes, accessory genes are represented in species that live in the niche, unique genes are unique to particular individual

]]> 2023-01-25 23:31:34 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899700 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899764 net tow

]]> 2023-01-25 23:31:42 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899764 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899796 Epifluorescence microscopy ]]> 2023-01-25 23:31:44 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899796 bacterial dilutions https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899889 2023-01-25 23:31:55 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899889 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899974 Direct counts and enrichment ]]> 2023-01-25 23:32:06 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456899974 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900107 manned submersibles (deep sea)]]> 2023-01-25 23:32:23 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900107 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900163 core genes: the minimum set of genes a group of organisms have
accessory gene: genes that are found in individual that are not required, most likely for niche adaptation
unique gene: genes that are not widely shared and have an unknown function, can be an accessory gene once we know what its purpose is]]> 2023-01-25 23:32:31 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900163 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900212 environmental sample processor  ]]> 2023-01-25 23:32:37 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900212 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900244 Niskin Bottles, Cores, Micron Net, Drone sampling, MBARI]]> 2023-01-25 23:32:43 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456900244 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456901196 Not all cells may lyse, organisms with identical 16s RNA may have different genomes ]]> 2023-01-25 23:34:20 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456901196 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456901235 FISH, PCR, Amplicon sequencing, RT-PCR ]]> 2023-01-25 23:34:24 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456901235 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456902124 Niskin bottles, net tows, Alvin, AUV ]]> 2023-01-25 23:36:15 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456902124 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456902265 Fixation of sampled cells 
Hybridization
Probes with the dyes attached enter cell and bind to complementary molecule
Washing of cells 
Cells are looked under microscope ]]> 2023-01-25 23:36:34 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456902265 coding sequences between start and stop codons that code for specific proteins. also determining their function. https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456902298 2023-01-25 23:36:38 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456902298 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456903526 If a nucleotide is off the primer won’t attach and pcr wont occur ]]> 2023-01-25 23:38:47 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456903526 A BAC library is when large pieces of environmental DNA are cloned into a special vector called a bacterial artificial chromosome. 40kbs pieces are common. Environmental gene clones are pieces of DNA (often PCR products of 500-1500 bp) that are cloned into a plasmid vector to create a "bank" of genes. Plasmid vectors tend to only accept smaller pieces of DNA compared to BACs. BAC construction does not require PCR. imoreno93 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456943713 2023-01-26 00:43:24 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456943713 There are two versions of RT-PCR: One could use the enzyme reverse transcriptase to make convert mRNA to DNA and then amplify the DNA with specific primers that would tell you if a specific organism is expressing a gene. You could also make amplify with more general primers and then sequence the pool of DNA to tell all the different organisms that are expressing that gene. imoreno93 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456945586 2023-01-26 00:45:49 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456945586 The stain used depends on the microscope set up as you need different filters to detect each (they have different excitation and emission wavelengths). They can be used depending on what you're looking for - DAPI is used to stain nuclei and eukaryotes and SYBR is much more sensitive so it can be used to look for viruses or much smaller cells. imoreno93 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456946446 2023-01-26 00:47:14 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456946446 The start sites of ORFs are more difficult to determine compared to stops because they are represented by slightly different nucleotides. Gene homology is used to determine correct length of the ORF. imoreno93 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456947719 2023-01-26 00:48:58 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456947719 1. Fix samples for hybridization (make sure probe connects to gene). 2. Add fluorescent oligonucleotide probes. 3. Wash cells with hybridization. 4. Do FISH analysis (look for fluorescence) using microscopy or flow cytometry. imoreno93 https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456949555 2023-01-26 00:51:41 UTC https://padlet.com/imoreno93/jiiuny712xnmf6hg/wish/2456949555