Journal: Frontiers in physiology

Article Title: Gut microbiota depletion minimally affects the daily voluntary wheel running activity and food anticipatory activity in female and male C57BL/6J mice.

doi: 10.3389/fphys.2023.1299474

Figure Lengend Snippet: FIGURE 1 The experimental procedure for microbiota depletion and feeding schedule. The days of beginning of ad libitum feeding (ALI, ALII), timed restricted feeding (TRF), food deprivation (FD) and collection of cecum and feces are indicated with the arrows.

Article Snippet: Extracted fecal DNA samples were shipped to Transnetyx Microbiome (Cordova, TN) for library preparation and whole-genome sequencing.

Techniques:

Journal: Frontiers in physiology

Article Title: Gut microbiota depletion minimally affects the daily voluntary wheel running activity and food anticipatory activity in female and male C57BL/6J mice.

doi: 10.3389/fphys.2023.1299474

Figure Lengend Snippet: FIGURE 5 Relative abundances of microbiota taxa from control and antibiotic-treated mice. Plot representing bacterial load in control (A) and antibiotics- treated (B) mice. Antibiotics depleted majority of gut microbiota. The “Mouse proportion” represents the number of reads that map to the One Codex database mouse genome divided by the total number of reads, while the “Bacterial proportion” represents the number of reads that map to bacteria at the taxonomic rank divided by the total number of reads. The “Other” category includes any reads classified as non-bacterial microorganisms. Taxonomic analysis showing gut microbiota population shifts at Family level. Relative abundance of top 15 families of microbial taxa in control (C), and antibiotics-treated (D) are shown. Lachnospiraceae (indicated as green) was present in all control mice but depleted in antibiotics treated mice. Erysipelotrichaceae was not detected in both control and antibiotics-treated mice. Top 15 orders and genus were shown in Supplementary Figure S5A–D. The number in the brackets represents NCBI taxonomic ID.

Article Snippet: Extracted fecal DNA samples were shipped to Transnetyx Microbiome (Cordova, TN) for library preparation and whole-genome sequencing.

Techniques: Control, Bacteria

Journal: Marine Life Science & Technology

Article Title: Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary

doi: 10.1007/s42995-023-00186-x

Figure Lengend Snippet: Spatial and seasonal variations in 18S-based OTU richness ( A–D ) and 16S-based ASV richness ( E–H ) of eukaryotic phytoplankton along the three transects. ASV, amplicon sequence variant; OTU, operational taxonomic unit

Article Snippet: The libraries of 16S and 18S rRNA amplicons were sequenced on the Illumina NovaSeq PE250 platform at a commercial company (Novogene, China).

Techniques: Amplification, Sequencing, Variant Assay

Journal: Marine Life Science & Technology

Article Title: Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary

doi: 10.1007/s42995-023-00186-x

Figure Lengend Snippet: The relationships between 18S-based OTU richness and the identified environmental factors that were most significant in the regression analyses ( A–D ). Also note that the weak correlations between 18S-based OTU and 16S-based ASV richness of the whole eukaryotic phytoplankton communities ( E ), and of individual phytoplankton groups ( F–J ). ASV, amplicon sequence variant; OTU, operational taxonomic unit; SRP, soluble reactive phosphorus

Article Snippet: The libraries of 16S and 18S rRNA amplicons were sequenced on the Illumina NovaSeq PE250 platform at a commercial company (Novogene, China).

Techniques: Amplification, Sequencing, Variant Assay

Journal: Marine Life Science & Technology

Article Title: Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary

doi: 10.1007/s42995-023-00186-x

Figure Lengend Snippet: Community composition of eukaryotic phytoplankton in surface (left panel), middle layer (middle panel) and bottom waters (right panel) in the Pearl River Estuary, as revealed by high throughput sequencing of nuclear 18S rRNA genes (upper row), plastid 16S rRNA genes (middle row), and pigment analysis (bottom row). Arrows and asterisks indicate the samples where hypoxia and blooms of pigmented dinophytes occurred

Article Snippet: The libraries of 16S and 18S rRNA amplicons were sequenced on the Illumina NovaSeq PE250 platform at a commercial company (Novogene, China).

Techniques: Next-Generation Sequencing

Journal: Marine Life Science & Technology

Article Title: Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary

doi: 10.1007/s42995-023-00186-x

Figure Lengend Snippet: Variations in phytoplankton community composition as characterized using nuclear 18S, plastid 16S, and pigment-based methods. A non-metric multidimensional scaling (NMDS) plot showing the variations in phytoplankton community structure resolved at the phylum level ( A ). A plot of principal component analysis showing that Haptophyta was underestimated in the 18S dataset, whereas diatoms and cryptophytes underestimated in the plastid 16S dataset ( B ). Scatter plots showing Pearson correlations between phytoplankton community distances based on 18S, plastid 16S, and pigments ( C–E )

Article Snippet: The libraries of 16S and 18S rRNA amplicons were sequenced on the Illumina NovaSeq PE250 platform at a commercial company (Novogene, China).

Techniques:

Journal: Marine Life Science & Technology

Article Title: Diversity, community structure, and quantity of eukaryotic phytoplankton revealed using 18S rRNA and plastid 16S rRNA genes and pigment markers: a case study of the Pearl River Estuary

doi: 10.1007/s42995-023-00186-x

Figure Lengend Snippet: Plots of canonical correspondence analysis (CCA) showing the environmental factors that significantly varied with the community structure of eukaryotic phytoplankton ( A–C ), and with relative abundances of major phytoplankton groups. The community structure was based on 18S ( A and D ), 16S rRNA genes ( B and E ), and pigments ( C and F ), and resolved at the OTU ( A ) and ASV ( B ) levels, and at major group levels ( C–E ). Note that different sets of environmental factors were selected for the phytoplankton communities characterized using these methods, nevertheless, more similar sets of environmental variables were selected in those characterized by 18S sequencing and pigment analysis. The water depths (surface, middle, and bottom layers) and months (July and November) of the collected samples are annotated in ( A–C ). Chl- a , chlorophyll a ; DIN, dissolved inorganic nitrogen; DSi, dissolved silicate; SRP, soluble reactive phosphorus

Article Snippet: The libraries of 16S and 18S rRNA amplicons were sequenced on the Illumina NovaSeq PE250 platform at a commercial company (Novogene, China).

Techniques: Sequencing

Journal: Journal of Personalized Medicine

Article Title: Bidirectional Relationship between HIV/HBV Infection and Comorbid Depression and/or Anxiety: A Systematic Review on Shared Biological Mechanisms

doi: 10.3390/jpm13121689

Figure Lengend Snippet: Preclinical and clinical studies investigating shared biological mechanisms in patients with HIV and depression/anxiety symptoms/syndromes.

Article Snippet: Taylor et al. 2023 USA [ ] , Cross-sectional study with151 participants (84 HIV+, 67 HIV−), subgrouped as follows: (a) HIV−/MDD− (3F, 20 M; 45.7 ± 13.5 years); (b) HIV−/MDD+ (14 F, 30 M; 45.0 ± 12.6 years); (c) HIV+/MDD− (2F, 18 M; 44.5 ± 14.3 years); and (d) HIV+/MDD+ (8F, 58 M; 46.1 ± 11.3 years). , Neuromedical and laboratory assessment , CIDI; BDI-II , Shallow-shotgun metagenomic sequencing of blood microbiome bacterial DNA. , The microbial composition did not differ between the PWH and the PWoH or between the participants with MDD and those without, though the patients with HIV infection and lifetime MDD showed a set of plasma microbiome community of the inflammatory classes, such as Flavobacteria and Nitrospira. The circulating plasma microbiome may increase the risk of MDD related to dysbiosis-induced inflammation in PWH..

Techniques: Injection, Modification, Gene Expression, Expressing, Western Blot, Transgenic Assay, Control, Saline, Cell Counting, Virus, Biomarker Discovery, Battery, Clinical Proteomics, Concentration Assay, Quantitative RT-PCR, Sampling, Activation Assay, Quantitation Assay, Derivative Assay, Infection, Medications, Immunohistochemical staining, Enzyme-linked Immunosorbent Assay, Combined Bisulfite Restriction Analysis Assay, Sequencing