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Macrogen sequencing service
Sequencing Service, supplied by Macrogen, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Amplification:

Article Title: Bacillus safensis and Bacillus haynesii , isolated from a saline-sodium environment: Resilience to multiple stresses and tolerance to nonsteroidal anti-inflammatory drugs, based on a genomic analysis and tolerance tests
Article Snippet: .. The amplified products are visualized on a 1 % agarose gel and revealed with ethidium bromide for 7 s. Macrogen Korea's sequencing service was selected to process the amplified products. .. The amplification of the 16S rRNA gene was performed using polymerase chain reaction (PCR) and universal primers 27F: 5′-AGA GTT TGA TCM TGG CTC AG-3′ and 1492R: 5′-TAC GGT TAC CTT GTT ACG ACT T-3′ Commercial Taq DNA polymerase (Meridian Bioscience, Bio-21,105) was used to perform the reaction.

Article Title: Tick-borne pathogens in Ixodes ricinus (Acari: Ixodidae) and Ixodes inopinatus × I. ricinus hybrids in Central Europe: no link to bird diversity or abundance.
Article Snippet: .. Amplicons were visualized under the UV light, and samples exhibiting an I. inopinatus or hybrid pattern, were subjected to an additional PCR targeting a longer fragment (824 bp) of the TROSPA gene (Hrazdilova et al. 2023) and sequenced in both directions using the amplification primers through Macrogen sequencing service (Macrogen Europe, The Netherlands). ..

Agarose Gel Electrophoresis:

Article Title: Bacillus safensis and Bacillus haynesii , isolated from a saline-sodium environment: Resilience to multiple stresses and tolerance to nonsteroidal anti-inflammatory drugs, based on a genomic analysis and tolerance tests
Article Snippet: .. The amplified products are visualized on a 1 % agarose gel and revealed with ethidium bromide for 7 s. Macrogen Korea's sequencing service was selected to process the amplified products. .. The amplification of the 16S rRNA gene was performed using polymerase chain reaction (PCR) and universal primers 27F: 5′-AGA GTT TGA TCM TGG CTC AG-3′ and 1492R: 5′-TAC GGT TAC CTT GTT ACG ACT T-3′ Commercial Taq DNA polymerase (Meridian Bioscience, Bio-21,105) was used to perform the reaction.

Sequencing:

Article Title: Bacillus safensis and Bacillus haynesii , isolated from a saline-sodium environment: Resilience to multiple stresses and tolerance to nonsteroidal anti-inflammatory drugs, based on a genomic analysis and tolerance tests
Article Snippet: .. The amplified products are visualized on a 1 % agarose gel and revealed with ethidium bromide for 7 s. Macrogen Korea's sequencing service was selected to process the amplified products. .. The amplification of the 16S rRNA gene was performed using polymerase chain reaction (PCR) and universal primers 27F: 5′-AGA GTT TGA TCM TGG CTC AG-3′ and 1492R: 5′-TAC GGT TAC CTT GTT ACG ACT T-3′ Commercial Taq DNA polymerase (Meridian Bioscience, Bio-21,105) was used to perform the reaction.

Article Title: Prevalence, Virulence Determinants, and Antimicrobial Resistance of Staphylococcus aureus and Escherichia coli Isolated from Computer Devices Used by Staff and Students at a Northern Thailand University
Article Snippet: .. Amplicons of the expected sizes (300 bp for S. aureus femA , 166 bp for E. coli uidA , 533 bp for mecA , and 304 bp for mecC ) were subsequently purified and sequenced by a commercial sequencing service (Macrogen Inc., Seoul, Republic of Korea). .. The obtained nucleotide sequences were analyzed for similarity using the BLASTn program available at the NCBI GenBank database (National Center for Biotechnology Information, Bethesda, MD, USA; https://blast.ncbi.nlm.nih.gov , accessed on 3 February 2026).

Article Title: Three new Pristimantis species in the subgenus Huicundomantis (Amphibia: Anura: Strabomantidae) from Reserva Biológica Cerro Plateado, southern Ecuador
Article Snippet: Genomic extraction, amplification, and sequencing were as described in ; briefly, from liver tissue preserved in 96% ethanol, we extracted DNA and amplified it through PCRs using Extract-N-AmpTM Tissue PCR Kit (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany) following the manufacturer’s protocol. .. PCR products were purified by PEG precipitation and sequenced at Macrogen Sequencing Service (Macrogen Inc., Seoul, Korea). ..

Article Title: Tick-borne pathogens in Ixodes ricinus (Acari: Ixodidae) and Ixodes inopinatus × I. ricinus hybrids in Central Europe: no link to bird diversity or abundance.
Article Snippet: .. Amplicons were visualized under the UV light, and samples exhibiting an I. inopinatus or hybrid pattern, were subjected to an additional PCR targeting a longer fragment (824 bp) of the TROSPA gene (Hrazdilova et al. 2023) and sequenced in both directions using the amplification primers through Macrogen sequencing service (Macrogen Europe, The Netherlands). ..

Article Title: Functional redundancy of translation-associated factors masks the role of YebC2 in Enterococcus faecalis.
Article Snippet: 1 Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Suipacha 590, Rosario, Argentina 2 Laboratorio de Biotecnología e Inocuidad de los Alimentos.. Área de Biotecnología de los Alimentos (FBioyF UNR Municipalidad de Granadero Baigorria), Sede Suipacha 590, Rosario, Argentina Abstract Enterococcus faecalis has two YebC paralogs, yebC1EF (EF0663) and yebC2EF (EF2866), with distinct roles.. While yebC1EF encodes a transcriptional regulator, yebC2EF was recently implicated in resolving ribosome stalling.

Article Title: Harnessing the Potential of Nodule Endophytic Bacteria to Improve Soybean Growth Under Saline Conditions.
Article Snippet: 1 Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan 2 Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan Abstract Soybean [Glycine max (L.) Merrill] is a major leguminous and oilseed crop known for high protein contents, fulfilling the nutritional demand, particularly in regions dominated by staple crops.. In recent years, salt stress has heavily limited crop productivity.. Salt-tolerant plant growth-promoting bacteria (PGPB) can better serve as biofertilizers for improved crop productivity under saline conditions.

Article Title: Prevalence, Virulence Determinants, and Antimicrobial Resistance of Staphylococcus aureus and Escherichia coli Isolated from Computer Devices Used by Staff and Students at a Northern Thailand University.
Article Snippet: .. Amplicons of the expected sizes (300 bp for S. aureus femA, 166 bp for E. coli uidA, 533 bp for mecA, and 304 bp for mecC) were subsequently purified and sequenced by a commercial sequencing service (Macrogen Inc., Seoul, Republic of Korea). .. The obtained nucleotide sequences were analyzed for similarity using the BLASTn program available at the NCBI GenBank database (National Center for Biotechnology Information, Bethesda, MD, USA; https://blast.ncbi.nlm.nih.gov, accessed on 3 February 2026).

ChIP-sequencing:

Article Title: TopBP1 orchestrates PU.1-IRF8 transcriptional programming of dendritic cell differentiation and Flt3L-driven tumor immunity.
Article Snippet: DNA was purified by phenol-chloroform extraction by mixing 1:1 with a phenol/chloroform/isoamyl alcohol (25:24:1) solution, and phenolchloroform residues were removed using phase lock gel tubes (Quantabio). .. DNA was then precipitated with pure ethanol at −20 °C, and chromatin immunoprecipitation sequencing (ChIP-seq) analysis was conducted by Macrogen. ..

Chromatin Immunoprecipitation:

Article Title: TopBP1 orchestrates PU.1-IRF8 transcriptional programming of dendritic cell differentiation and Flt3L-driven tumor immunity.
Article Snippet: DNA was purified by phenol-chloroform extraction by mixing 1:1 with a phenol/chloroform/isoamyl alcohol (25:24:1) solution, and phenolchloroform residues were removed using phase lock gel tubes (Quantabio). .. DNA was then precipitated with pure ethanol at −20 °C, and chromatin immunoprecipitation sequencing (ChIP-seq) analysis was conducted by Macrogen. ..

Purification:

Article Title: Prevalence, Virulence Determinants, and Antimicrobial Resistance of Staphylococcus aureus and Escherichia coli Isolated from Computer Devices Used by Staff and Students at a Northern Thailand University
Article Snippet: .. Amplicons of the expected sizes (300 bp for S. aureus femA , 166 bp for E. coli uidA , 533 bp for mecA , and 304 bp for mecC ) were subsequently purified and sequenced by a commercial sequencing service (Macrogen Inc., Seoul, Republic of Korea). .. The obtained nucleotide sequences were analyzed for similarity using the BLASTn program available at the NCBI GenBank database (National Center for Biotechnology Information, Bethesda, MD, USA; https://blast.ncbi.nlm.nih.gov , accessed on 3 February 2026).

Article Title: Three new Pristimantis species in the subgenus Huicundomantis (Amphibia: Anura: Strabomantidae) from Reserva Biológica Cerro Plateado, southern Ecuador
Article Snippet: Genomic extraction, amplification, and sequencing were as described in ; briefly, from liver tissue preserved in 96% ethanol, we extracted DNA and amplified it through PCRs using Extract-N-AmpTM Tissue PCR Kit (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany) following the manufacturer’s protocol. .. PCR products were purified by PEG precipitation and sequenced at Macrogen Sequencing Service (Macrogen Inc., Seoul, Korea). ..

Article Title: Prevalence, Virulence Determinants, and Antimicrobial Resistance of Staphylococcus aureus and Escherichia coli Isolated from Computer Devices Used by Staff and Students at a Northern Thailand University.
Article Snippet: .. Amplicons of the expected sizes (300 bp for S. aureus femA, 166 bp for E. coli uidA, 533 bp for mecA, and 304 bp for mecC) were subsequently purified and sequenced by a commercial sequencing service (Macrogen Inc., Seoul, Republic of Korea). .. The obtained nucleotide sequences were analyzed for similarity using the BLASTn program available at the NCBI GenBank database (National Center for Biotechnology Information, Bethesda, MD, USA; https://blast.ncbi.nlm.nih.gov, accessed on 3 February 2026).

Polymerase Chain Reaction:

Article Title: Three new Pristimantis species in the subgenus Huicundomantis (Amphibia: Anura: Strabomantidae) from Reserva Biológica Cerro Plateado, southern Ecuador
Article Snippet: Genomic extraction, amplification, and sequencing were as described in ; briefly, from liver tissue preserved in 96% ethanol, we extracted DNA and amplified it through PCRs using Extract-N-AmpTM Tissue PCR Kit (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany) following the manufacturer’s protocol. .. PCR products were purified by PEG precipitation and sequenced at Macrogen Sequencing Service (Macrogen Inc., Seoul, Korea). ..

Article Title: Tick-borne pathogens in Ixodes ricinus (Acari: Ixodidae) and Ixodes inopinatus × I. ricinus hybrids in Central Europe: no link to bird diversity or abundance.
Article Snippet: .. Amplicons were visualized under the UV light, and samples exhibiting an I. inopinatus or hybrid pattern, were subjected to an additional PCR targeting a longer fragment (824 bp) of the TROSPA gene (Hrazdilova et al. 2023) and sequenced in both directions using the amplification primers through Macrogen sequencing service (Macrogen Europe, The Netherlands). ..



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(A) Architecture of the recombinase-based memory switch. The input module (pSwitch) contains IPTG- and arabinose-inducible promoters driving the expression of HbiF and FimE, respectively. The output module (pReporter) contains recombinase recognition sites flanking a constitutive promoter (Ptrc*) controlling RFP and GFP expression. Site-specific <t>DNA</t> inversion between the inverted repeats (IRL/IRR) reconfigures the recombination sites, reversing the promoter orientation and thereby toggling expression between RFP and GFP . (B) Flow cytometry analysis of cells initialized in the Green-On state and analyzed on day 3. The percentages of Red, uncommitted, and Green cells are reported as indicated. Red circles indicate the effect of recombinase leakiness and non-orthogonality. (C) Flow cytometry analysis of cells initialized in the Green-On state and switched to the Red-On state on day 3. (D) Flow cytometry analysis of cells initialized in the Red-On state and analyzed on day 3. (E) Flow cytometry analysis of cells initialized in the Red-On state and switched to the Green-On state on day 3.
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(A) Corallimorpharian mucus collection. After initial salt water dripped off animals and plates, mucus was collected from adult Corallimorpharian animals by tilting over 1.5 mL centrifuge tubes and collecting the run-off. B,C) R. florida mucus exhibit consistently higher CFU counts than those that harbored seawater. Corallimorph mucus (A) and surrounding sea water (C) were cultured on Marine Agar plates and the number of colony forming units were quantified. ( D) Corallimorpharian mucus harbors morphologically diverse bacterial isolates. Colonies isolated from R. florida mucus exhibited substantial variation in pigmentation and morphology, including dark purple/black (A), translucent cream (B-D), white (E), and peach (F) morphotypes. Isolates also differed in colony architecture and growth characteristics. Among these, one isolate displayed an unusual agar-pitting phenotype (G), suggesting extracellular agar-degrading activity. ( E,F) R. florida were infected with A2 Vibrio . Clonal polyps from control treatment (E) and high bacterial exposure (F) were pooled in equal quantities for mRNA library construction and <t>sequencing</t> using MiSeq technology (Illumina).
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(A) Corallimorpharian mucus collection. After initial salt water dripped off animals and plates, mucus was collected from adult Corallimorpharian animals by tilting over 1.5 mL centrifuge tubes and collecting the run-off. B,C) R. florida mucus exhibit consistently higher CFU counts than those that harbored seawater. Corallimorph mucus (A) and surrounding sea water (C) were cultured on Marine Agar plates and the number of colony forming units were quantified. ( D) Corallimorpharian mucus harbors morphologically diverse bacterial isolates. Colonies isolated from R. florida mucus exhibited substantial variation in pigmentation and morphology, including dark purple/black (A), translucent cream (B-D), white (E), and peach (F) morphotypes. Isolates also differed in colony architecture and growth characteristics. Among these, one isolate displayed an unusual agar-pitting phenotype (G), suggesting extracellular agar-degrading activity. ( E,F) R. florida were infected with A2 Vibrio . Clonal polyps from control treatment (E) and high bacterial exposure (F) were pooled in equal quantities for mRNA library construction and <t>sequencing</t> using MiSeq technology (Illumina).
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(A) Corallimorpharian mucus collection. After initial salt water dripped off animals and plates, mucus was collected from adult Corallimorpharian animals by tilting over 1.5 mL centrifuge tubes and collecting the run-off. B,C) R. florida mucus exhibit consistently higher CFU counts than those that harbored seawater. Corallimorph mucus (A) and surrounding sea water (C) were cultured on Marine Agar plates and the number of colony forming units were quantified. ( D) Corallimorpharian mucus harbors morphologically diverse bacterial isolates. Colonies isolated from R. florida mucus exhibited substantial variation in pigmentation and morphology, including dark purple/black (A), translucent cream (B-D), white (E), and peach (F) morphotypes. Isolates also differed in colony architecture and growth characteristics. Among these, one isolate displayed an unusual agar-pitting phenotype (G), suggesting extracellular agar-degrading activity. ( E,F) R. florida were infected with A2 Vibrio . Clonal polyps from control treatment (E) and high bacterial exposure (F) were pooled in equal quantities for mRNA library construction and <t>sequencing</t> using MiSeq technology (Illumina).
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Step 1 ) The sensors are printed with biodegradable PHBV, poly(3-hydroxybutuyrate- co -3-hydroxyvalerate), on one side and non-biodegradable PMMA, poly(methyl methacrylate) on the other side as a control. Step 2 ) UV-sterilized sensors are inserted into soil mesocosms and monitor PHBV degradation in real-time as an increase in resistance, which we normalize to the non-degraded PMMA. Step 3 ) At the end of the mesocosm incubation, the sensors are removed and we can summarise the PHBV degradation signal to identify which soils have the highest capacity to degrade PHBV. Step 4 ) PHBV and PMMA material from sensors incubated in the highest PHBV-degrading soils are scraped off and used as starting material for culture-independent ( Step 5 , left panel) and culture-dependent ( Step 6 , right panel) approaches to identify novel PHBV degraders. Step 5, left ) We used the PHBV and PMMA material from high degrading soils for 16S rRNA and ITS marker gene <t>sequencing</t> to identify microbes enriched on degraded PHBV compared to non-degraded PMMA from each in situ sensor. Step 5, right ) We also used the PHBV material from high degrading soils to isolate novel PHBV degraders on agar plates with a PHBV overlay (inset). Isolates that formed clearing zones on plates were cultured in liquid media to measure their continued capacity to degrade PHBV. We also measured the respiration rates of isolates growing with PHBV as their sole carbon source to confirm PHBV catabolism.
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Image Search Results


(A) Architecture of the recombinase-based memory switch. The input module (pSwitch) contains IPTG- and arabinose-inducible promoters driving the expression of HbiF and FimE, respectively. The output module (pReporter) contains recombinase recognition sites flanking a constitutive promoter (Ptrc*) controlling RFP and GFP expression. Site-specific DNA inversion between the inverted repeats (IRL/IRR) reconfigures the recombination sites, reversing the promoter orientation and thereby toggling expression between RFP and GFP . (B) Flow cytometry analysis of cells initialized in the Green-On state and analyzed on day 3. The percentages of Red, uncommitted, and Green cells are reported as indicated. Red circles indicate the effect of recombinase leakiness and non-orthogonality. (C) Flow cytometry analysis of cells initialized in the Green-On state and switched to the Red-On state on day 3. (D) Flow cytometry analysis of cells initialized in the Red-On state and analyzed on day 3. (E) Flow cytometry analysis of cells initialized in the Red-On state and switched to the Green-On state on day 3.

Journal: bioRxiv

Article Title: Engineering Persistent and Rewritable Genetic Memory in Bacteria through Multiscale Plasmid Competition

doi: 10.64898/2026.09.18.752696

Figure Lengend Snippet: (A) Architecture of the recombinase-based memory switch. The input module (pSwitch) contains IPTG- and arabinose-inducible promoters driving the expression of HbiF and FimE, respectively. The output module (pReporter) contains recombinase recognition sites flanking a constitutive promoter (Ptrc*) controlling RFP and GFP expression. Site-specific DNA inversion between the inverted repeats (IRL/IRR) reconfigures the recombination sites, reversing the promoter orientation and thereby toggling expression between RFP and GFP . (B) Flow cytometry analysis of cells initialized in the Green-On state and analyzed on day 3. The percentages of Red, uncommitted, and Green cells are reported as indicated. Red circles indicate the effect of recombinase leakiness and non-orthogonality. (C) Flow cytometry analysis of cells initialized in the Green-On state and switched to the Red-On state on day 3. (D) Flow cytometry analysis of cells initialized in the Red-On state and analyzed on day 3. (E) Flow cytometry analysis of cells initialized in the Red-On state and switched to the Green-On state on day 3.

Article Snippet: DNA sequencing used Plasmidsaurus DNA whole plasmid sequencing service.

Techniques: Expressing, Flow Cytometry, Analysis

(A) Corallimorpharian mucus collection. After initial salt water dripped off animals and plates, mucus was collected from adult Corallimorpharian animals by tilting over 1.5 mL centrifuge tubes and collecting the run-off. B,C) R. florida mucus exhibit consistently higher CFU counts than those that harbored seawater. Corallimorph mucus (A) and surrounding sea water (C) were cultured on Marine Agar plates and the number of colony forming units were quantified. ( D) Corallimorpharian mucus harbors morphologically diverse bacterial isolates. Colonies isolated from R. florida mucus exhibited substantial variation in pigmentation and morphology, including dark purple/black (A), translucent cream (B-D), white (E), and peach (F) morphotypes. Isolates also differed in colony architecture and growth characteristics. Among these, one isolate displayed an unusual agar-pitting phenotype (G), suggesting extracellular agar-degrading activity. ( E,F) R. florida were infected with A2 Vibrio . Clonal polyps from control treatment (E) and high bacterial exposure (F) were pooled in equal quantities for mRNA library construction and sequencing using MiSeq technology (Illumina).

Journal: bioRxiv

Article Title: Comparative genomics and microbiome profiling reveal a conserved Vibrio rich mucus microbiota of the Florida false coral ( Ricordea florida )

doi: 10.64898/2026.09.17.752451

Figure Lengend Snippet: (A) Corallimorpharian mucus collection. After initial salt water dripped off animals and plates, mucus was collected from adult Corallimorpharian animals by tilting over 1.5 mL centrifuge tubes and collecting the run-off. B,C) R. florida mucus exhibit consistently higher CFU counts than those that harbored seawater. Corallimorph mucus (A) and surrounding sea water (C) were cultured on Marine Agar plates and the number of colony forming units were quantified. ( D) Corallimorpharian mucus harbors morphologically diverse bacterial isolates. Colonies isolated from R. florida mucus exhibited substantial variation in pigmentation and morphology, including dark purple/black (A), translucent cream (B-D), white (E), and peach (F) morphotypes. Isolates also differed in colony architecture and growth characteristics. Among these, one isolate displayed an unusual agar-pitting phenotype (G), suggesting extracellular agar-degrading activity. ( E,F) R. florida were infected with A2 Vibrio . Clonal polyps from control treatment (E) and high bacterial exposure (F) were pooled in equal quantities for mRNA library construction and sequencing using MiSeq technology (Illumina).

Article Snippet: Some isolates were re-sequenced using the Plasmidsaurus Whole Genome Sequencing service (Oxford Nanopore, R10.4.1 long-reads and de novo genome assembly).

Techniques: Cell Culture, Isolation, Morphology, Cream, Activity Assay, Infection, Control, Sequencing

A. Relative abundance (%) of bacteria Genera collected from polyps from distinct tank systems reveals a dominance of Vibrio . Columns of each bar graph represent a polyp (A or B) and tank collected from is noted with the number. B. Polyps from the same tank show no difference in bacterial assemblage. A principal component analysis (PCA) reveals no differences in structure of bacterial communities between tank systems (12, 14, and 15 represented by blue, green and purple circles). X and Y axes show Principal Component 1 and Principal Component 2 that explain 56% and 22% of the total variance, respectively. (C). Shared and unique ASVs among corallimorph-associated bacterial communities. UpSet plot showing the overlap of amplicon sequence variants (ASVs) among Tanks 12, 14, and 15. An ASV was considered present within a tank only if it was detected in both animals sampled from that tank. Numbers indicate ASVs unique to individual tanks or shared among multiple tanks.

Journal: bioRxiv

Article Title: Comparative genomics and microbiome profiling reveal a conserved Vibrio rich mucus microbiota of the Florida false coral ( Ricordea florida )

doi: 10.64898/2026.09.17.752451

Figure Lengend Snippet: A. Relative abundance (%) of bacteria Genera collected from polyps from distinct tank systems reveals a dominance of Vibrio . Columns of each bar graph represent a polyp (A or B) and tank collected from is noted with the number. B. Polyps from the same tank show no difference in bacterial assemblage. A principal component analysis (PCA) reveals no differences in structure of bacterial communities between tank systems (12, 14, and 15 represented by blue, green and purple circles). X and Y axes show Principal Component 1 and Principal Component 2 that explain 56% and 22% of the total variance, respectively. (C). Shared and unique ASVs among corallimorph-associated bacterial communities. UpSet plot showing the overlap of amplicon sequence variants (ASVs) among Tanks 12, 14, and 15. An ASV was considered present within a tank only if it was detected in both animals sampled from that tank. Numbers indicate ASVs unique to individual tanks or shared among multiple tanks.

Article Snippet: Some isolates were re-sequenced using the Plasmidsaurus Whole Genome Sequencing service (Oxford Nanopore, R10.4.1 long-reads and de novo genome assembly).

Techniques: Bacteria, Analysis, Amplification, Sequencing

HeLa:Cas9 cells in 10cm plates were transfected with overexpression constructs for HPV16L2, encoding a C-terminal HA tag, and either an overexpression construct for PLCδ4 or PLCγ1, both containing the sequence for both C-terminal FLAG tag and c-Myc tag, or pCMV6, an empty vector control. Transfected cells were harvested 24h post-transfection, lysed in buffer containing 1% NP40 and 0.1% SDS, and then (cleared) lysates were incubated with magnetic beads coupled to anti-HA antibodies to pull down L2. Co-immunoprecipitation (CoIP) of PLCδ4 in bead elutions (“Elutes”) was determined using Western blot. Western blotting against the HA and c-Myc tags was used to confirm the presence of L2, PLCδ4, and PLCγ1 in “elutes” and “cleared lysates”. Blots are representative of three independent experiments ( N =3).

Journal: bioRxiv

Article Title: HPV16 Utilizes Phospholipase C(s) for its Genome Egress

doi: 10.64898/2026.09.03.749318

Figure Lengend Snippet: HeLa:Cas9 cells in 10cm plates were transfected with overexpression constructs for HPV16L2, encoding a C-terminal HA tag, and either an overexpression construct for PLCδ4 or PLCγ1, both containing the sequence for both C-terminal FLAG tag and c-Myc tag, or pCMV6, an empty vector control. Transfected cells were harvested 24h post-transfection, lysed in buffer containing 1% NP40 and 0.1% SDS, and then (cleared) lysates were incubated with magnetic beads coupled to anti-HA antibodies to pull down L2. Co-immunoprecipitation (CoIP) of PLCδ4 in bead elutions (“Elutes”) was determined using Western blot. Western blotting against the HA and c-Myc tags was used to confirm the presence of L2, PLCδ4, and PLCγ1 in “elutes” and “cleared lysates”. Blots are representative of three independent experiments ( N =3).

Article Snippet: PLCβ4 and PLCδ4 gene edits in selected clonal HeLa cells were further confirmed via sequencing with Plasmidsaurus sequencing services using Oxford Nanopore Technology.

Techniques: Transfection, Over Expression, Construct, Sequencing, FLAG-tag, Plasmid Preparation, Control, Incubation, Magnetic Beads, Co-Immunoprecipitation Assay, Western Blot

Step 1 ) The sensors are printed with biodegradable PHBV, poly(3-hydroxybutuyrate- co -3-hydroxyvalerate), on one side and non-biodegradable PMMA, poly(methyl methacrylate) on the other side as a control. Step 2 ) UV-sterilized sensors are inserted into soil mesocosms and monitor PHBV degradation in real-time as an increase in resistance, which we normalize to the non-degraded PMMA. Step 3 ) At the end of the mesocosm incubation, the sensors are removed and we can summarise the PHBV degradation signal to identify which soils have the highest capacity to degrade PHBV. Step 4 ) PHBV and PMMA material from sensors incubated in the highest PHBV-degrading soils are scraped off and used as starting material for culture-independent ( Step 5 , left panel) and culture-dependent ( Step 6 , right panel) approaches to identify novel PHBV degraders. Step 5, left ) We used the PHBV and PMMA material from high degrading soils for 16S rRNA and ITS marker gene sequencing to identify microbes enriched on degraded PHBV compared to non-degraded PMMA from each in situ sensor. Step 5, right ) We also used the PHBV material from high degrading soils to isolate novel PHBV degraders on agar plates with a PHBV overlay (inset). Isolates that formed clearing zones on plates were cultured in liquid media to measure their continued capacity to degrade PHBV. We also measured the respiration rates of isolates growing with PHBV as their sole carbon source to confirm PHBV catabolism.

Journal: bioRxiv

Article Title: Identification of soil microbes associated with real-time plastic degradation using in situ conductivity sensors

doi: 10.64898/2026.08.16.745074

Figure Lengend Snippet: Step 1 ) The sensors are printed with biodegradable PHBV, poly(3-hydroxybutuyrate- co -3-hydroxyvalerate), on one side and non-biodegradable PMMA, poly(methyl methacrylate) on the other side as a control. Step 2 ) UV-sterilized sensors are inserted into soil mesocosms and monitor PHBV degradation in real-time as an increase in resistance, which we normalize to the non-degraded PMMA. Step 3 ) At the end of the mesocosm incubation, the sensors are removed and we can summarise the PHBV degradation signal to identify which soils have the highest capacity to degrade PHBV. Step 4 ) PHBV and PMMA material from sensors incubated in the highest PHBV-degrading soils are scraped off and used as starting material for culture-independent ( Step 5 , left panel) and culture-dependent ( Step 6 , right panel) approaches to identify novel PHBV degraders. Step 5, left ) We used the PHBV and PMMA material from high degrading soils for 16S rRNA and ITS marker gene sequencing to identify microbes enriched on degraded PHBV compared to non-degraded PMMA from each in situ sensor. Step 5, right ) We also used the PHBV material from high degrading soils to isolate novel PHBV degraders on agar plates with a PHBV overlay (inset). Isolates that formed clearing zones on plates were cultured in liquid media to measure their continued capacity to degrade PHBV. We also measured the respiration rates of isolates growing with PHBV as their sole carbon source to confirm PHBV catabolism.

Article Snippet: DNA aliquots from two of our isolates, Streptomyces sp. [2CO Garden Isolate], Lysinibacillus sp. [2CO Garden Isolate] were sequenced by Plasmidsaurus using their bacterial genome sequencing service.

Techniques: Control, Incubation, Marker, Sequencing, In Situ, Cell Culture