1. Today HK Science *.ppt Reports, snail/parasite or fungus
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*.ppt
Reports, snail/parasite or fungus

2. For DNA to be read, replicated or repaired, DNA molecules must open themselves. This happens when the cells use a catalytic protein to create a hydrophobic environment around the molecule.

7. SNAIL AND PARASITES BIOLOGY
DNA
“identity, possibilities”
phylogenetics
CTAB/DNAzol
gel electrophoresis
nanodrop spec
Illumina (full)
genome sequencing
PCR rDNA/mito
Qubit Fluorometry
Covaris fragmentation
Ampure (fragment collection)
Kapa DNA library preparation kit
Pippin size selection
QC Bioanalyzer, Qubit, qPCR
Illumina run
TA cloning, B/W screening
electrophoresis
Pure Link plasmid extraction Restriction digests
direct sequencing
M13 sequencing
Sequence ID (BLAST)
editing
Primer design, walking
Galaxy
QC Data file
(MT) genome assembly
Mitos, manual annotation
Gene annotation
Phylogenetics
GenBank submission

8. *.ppt

9. Content Final Report Snails and Parasites
Intro Trematodes cause infectious diseases of human and animals. Characterization of snails and their trematodes present at Shady Lakes. (Potential risks for…) Methods Snail collection, inspection for parasites, broad ID on morphology. DNA extraction, Ancylid, new observation no parasite observed, but investigated to evaluate ID, potential for parasite transmission, conserved primer PCR amplification, sequencing Sanger (direct/cloning, primer walking) Contig assembly COI, 16S, 28S. Illumina sequencing, MITOBIM assembly, MITOS annotation. BLAST and Phylogenetic assembly for ID. Sequence submission to GenBank. Results Snails collected, types of parasites observed initial ID. Sequences obtained from snails and parasites. Illumina data, assembly of complete mt genomes snails and parasites. Data submitted to GenBank. BLAST and Phylogenetics of 16S and COI ID snails as v,w,x,y,z (show a tree); 28S or Mt genomes ID parasites a,b,c,d of the snails, respectively. Discussion Presence of snails and vertebrates great potential for trematode life cycles. L, P, AP can transmit several diseases. Parasite-snail associations reported previously? ID Sanger versus Illumina more specific? Specific or more general associations? Types of disease in vertebrate hosts. Risks at Shady lakes. …. Literature cited, figure/table etc.

10. Content Final Report - Lung Fungi
Intro Until very recently, healthy mammalian lungs were thought to represent a sterile environment. It is now known that they possess a true microbiome. Here, we are addressing the question of the fungal component of the lung microbiome (mycobiome) Methods a. Animals were collected in California by James Patton, Univ of California Berkeley (see spreadsheet). b. Lung fragments were plated onto YG agar medium with streptomycin (10 mg/liter) and chloramphenicol (50 mg/liter) to prevent bacterial contamination. YG agar (per liter) has 10 g yeast extract, 20 g glucose and 15 g bacto agar. c. DNA was extracted from fungal colonies using the CTAB procedure d. Fungal ITS sequences were amplified using primers ITS1-F and ITS4 e. ITS PCR fragments were sequenced (2 reactions per PCR) using ITS1-F as the forward primer and ITS4 as the reverse reaction. f. ITS sequences were assembled and used for Blast searches to identify the fungi recovered. Questions for Results Approximately how many animals produced at least one colony? Approximately how many lung fragments produced at least one fungal colony? What fungi were recovered? Questions for Discussion What is the significance of the fact that most lung fragments possessed at least one fungal species? Which of the fungi recovered here have been shown to produce infections in humans or non-human animals? What portion of the lungs produced colonies of Emmonsia parva (=Blastomyces parvus, = Haplosporangium parvum)? What is the significance of this?