Polymerase Chain Reaction:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
Purification:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
Sequencing:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
Software:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
Microscopy:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
Fluorescence:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
Food & Beverages:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
Concentration Assay:Article Title: Protocol for spatial sampling and monitoring infection disease dynamics and pathogen spread in social ambrosia beetle colonies.
Article Snippet: MATERIALS AND EQUIPMENT Continued REAGENT or RESOURCE SOURCE IDENTIFIER Cetyl trimethyl ammonium bromide (CTAB) Sigma-Aldrich Cat# 57090 Tissue-Tek® O.C.T. .. Compound SAKURA Cat#4583 DAPI Vector Laboratories Inc., Newark, CA, USA Cat#H-1200-10 Phalloidin Vector Laboratories Inc., Newark, CA, USA Cat#H-1600-10 23 Taq® PCR SuperMix APExBIO, Houston, TX, USA Cat#K1034 Critical commercial assays DNeasy Plant Mini Kit Qiagen Cat# 69106 GeneJET PCR Purification Kit Thermo Fisher Scientific Cat# K0701 Vectashield Hardset Antifade Mounting Medium with DAPI and Phalloidin Vector Laboratories Cat# H-1500-10 Sabouraud dextrose agar (SDA) Ward’s Science Cat#470227-486 Czapek–Dox agar (CZA) DifcoTM Cat#233810 Deposited data Neocosmospora sp. Xa1 TEF1-α sequence This paper GenBank: PV220985 Experimental models: organisms/strains Xyleborus affinis beetles Laboratory colony, University of Illinois Chicago N/A Oligonucleotides 3 ′ side TEF1-α (983F) 5 ′ -GCYCCYGGHCAYCGTGAYTTYAT-3 ′ See step-by-step method details 3 ′ side TEF1-α (2218R) 5 ′ -ATGACACCRACRGCRACRGTYTG-3 ′ See step-by-step method details 5 ′ side TEF1-α (EFT1) 5 ′ -ATGGGTAAGGARGACAAGAC-3 ′ See step-by-step method details 5 ′ side TEF1-α (1567R) 5 ′ -ACHGTRCCRATACCACCSATCTT-3 ′ See step-by-step method details Software and algorithms SAS JMP Pro version 18.0.1 SAS Institute https://www.jmp.com OASIS version 2 survival analysis tool Online tool https://sbi.postech.ac.kr/oasis2/ Topali version 2.5 University of Edinburgh http://www.topali.org/ BioEdit Ibis Biosciences http://www.mbio.ncsu.edu/BioEdit/bioedit.html MAFFT Katoh Lab https://mafft.cbrc.jp/alignment/software/ MrBayes Huelsenbeck Lab http://mrbayes.sourceforge.net/ FigTree Institute of Evolutionary Biology, Univ. of Edinburgh http://tree.bio.ed.ac.uk/software/figtree/ BZ-X800 Analyzer software Keyence Corporation N/A Other Leica DM5000 B Microscope Leica Microsystems N/A BZ-X810 Fluorescence Microscope Keyence Corporation N/A Hemocytometer Neubauer-improved, Lauda-Kö nigshofen, Germany N/A FastPrep-24 homogenizer MP Biomedicals, USA N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany N/A C1000 TouchTM thermal cycler Bio-Rad Laboratories, Hercules, CA, USA N/A White sheet N/A Bright white light N/A NanoPhotometer® NP80 Implen GmbH, Munich, Germany See method Recipe for Beetle Food Reagent Final concentration (w/v) Amount Wood flour 12% 60 g Sweetgum sawdust (coarse) 3% 15 g Agar 4% 20 g (Continued on next page) 8 STAR Protocols 7, 104375, March 20, 2026 Note: These ingredients can be stored at 25 ◦ C. Note: The PCR buffer and primers should be stored at − 20 ◦ C for up to 6 months. .. Ex-colony plate assays of fungal (Metarhizium) infections of beetles and conidiation of M. anisopliae and M. robertsii on X. affinis Timing: 3–4 h active time, plus 12–18 h incubation for germination assessment Continued Reagent Final concentration (w/v) Amount Sucrose 2% 10 g Corn starch 1% 5 g Casein 1% 5 g Yeast extract 1% 5 g Wesson salt mixture 0.2% 1 g Streptomycin sulfate 0.07% 0.35 g Ethanol (95%) N/A 5 mL Wheat germ oil N/A 2.5 mL Sterile distilled water N/A To 500 mL Total N/A 500 mL Recipe for PCR analyses Reagent Volume per reaction (25 μL) 23 Taq® PCR SuperMix (APExBIO) 6.5 μL Forward primer 2.5 μL Reverse primer 2.5 μL DNA template 2 μL Sterile distilled water 11.5 μL Total volume 25 μL PCR cycling conditions for TEF1-α (3 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 2 min 1 Denaturation 94 30 s 10 Annealing (touchdown) 66 → 56 30 s Extension 72 1 min Denaturation 94 30 s 40 Annealing 56 30 s Extension 72 1 min Final extension 72 10 min 1 Hold 4 ∞ — PCR cycling conditions for TEF1-α (5 ′ region) Step Temperature ( ◦ C) Time Cycles Initial denaturation 94 5 min 1 Denaturation 94 1 min 35 Annealing 55 50 s Extension 72 3 min Final extension 72 10 min 1 Hold 4 ∞ — STAR Protocols 7, 104375, March 20, 2026 9 This section describes the preparation, quantification, and viability assessment of M. anisopliae conidia harvested from sporulating colonies, followed by standardized immersion-based exposure of X. affinis adults.
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