Journal: bioRxiv

Article Title: Efferocytosis Remodels Osteoclast Metabolism and Enhances Antibacterial Defense

doi: 10.64898/2026.10.13.759003

Figure Lengend Snippet: a , Heatmap showing expression of osteoclast-associated genes, TAM receptor family genes, and macrophage-associated genes during murine osteoclast differentiation (GSE147174). BMM, bone marrow-derived macrophages (M-CSF, 2 days); pOC, pre-osteoclasts (BMM + RANKL for 1 day); mOC, mature osteoclasts (BMM + RANKL for 3 days). n = 3 bulk RNA-seq samples per differentiation stage; each heatmap column represents one sample. b , Representative gel electrophoresis images of PCR products for Tyro3 , Axl , Mertk , and Actb in BMMs, pOCs, and mOCs. c , Quantitative PCR analysis of Tyro3 , Axl , and Mertk transcript levels in BMMs, pOCs and mOCs. d,e , Immunoblot analysis of AXL, MERTK, and β-actin expression in BMM, pOC, and mOC ( d ), with densitometric quantification ( e ). f,g , Immunofluorescence images of mouse femoral sections showing MERTK ( f ) and AXL ( g ) expression in bone-resident osteoclasts. MERTK and AXL are shown in red in f and g , respectively; CTSK is shown in green, and nuclei are shown in blue (DAPI). Quantification shows the number of receptor-positive multinucleated osteoclasts per bone perimeter and the percentage of osteoclasts positive for MERTK or AXL. Scale bars, 20 µm. h , Flow cytometric quantification of apoptotic neutrophil (aN) efferocytosis by BMMs and osteoclasts. i , Representative immunofluorescence images of BMMs and osteoclasts incubated with apoptotic neutrophils (aN). Phagocytes are shown in green, apoptotic neutrophils in red, and nuclei stained with DAPI (blue). White arrows indicate apoptotic cells with pyknotic nuclei, and yellow arrows indicate aN. Scale bars, 50 µm. j , Quantification of apoptotic neutrophil uptake by BMMs and osteoclasts following siRNA-mediated depletion of Axl or Mertk . The phagocytosis index was calculated as experimental engulfment (%) divided by control engulfment (%). Data are presented as mean ± s.d. Statistical significance was assessed using two-tailed unpaired t -tests ( h ) and one-way ANOVA followed by Tukey’s multiple comparisons test ( c,e,j ). n = 3 independent biological samples per group ( c,e,h,j ) and n = 5 mice ( f,g ). Each point represents one biological sample or one mouse, respectively; linked points in f,g denote measurements from the same mouse.

Article Snippet: Sections were incubated overnight at 4°C with primary antibodies against Ly6G (Servicebio; GB11229), CTSK (Santa Cruz Biotechnology; sc-48353), MERTK (Proteintech; 27900-1-AP), AXL (MedChemExpress; HY-P81198), phospho-MLKL (Ser345) (Abcam; ab196436), and Staphylococcus aureus (Abcam; ab20920), followed by incubation with the corresponding fluorophore-conjugated secondary antibodies.

Techniques: Expressing, Derivative Assay, RNA Sequencing, Gel Electrophoresis, Real-time Polymerase Chain Reaction, Analysis, Western Blot, Immunofluorescence, Incubation, Staining, Control, Two Tailed Test

Journal: Applied and Environmental Microbiology

Article Title: Contrasting Microbiome Dynamics of Putative Denitrifying Bacteria in Two Octocoral Species Exposed to Dissolved Organic Carbon (DOC) and Warming

doi: 10.1128/AEM.01886-21

Figure Lengend Snippet: Community compositions and relative abundances of putative denitrifiers in corals X. umbellata and P. flava over the course of the experiment. (a) Relative proportions of denitrifier genera of corals X. umbellata and P. flava inferred by nirS in-silico PCR in relation to the total bacterial community from 16S rRNA gene sequencing. (b) Relative fold changes in copy numbers of nirS gene referenced to 16S rRNA gene and in relation to the day 0 control samples ( n = 3) of corals X. umbellata and P. flava . Values are means ± SD, and the asterisk indicates statistically significant differences (* P < 0.05).

Article Snippet: The 16S rRNA gene amplicon sequencing was conducted at LGC genomics (Berlin, Germany).

Techniques: In Silico, Sequencing

Journal: Clinical Case Reports

Article Title: Identification of EPCAM mutation: clinical use of microarray

doi: 10.1002/ccr3.914

Figure Lengend Snippet: Microarray analysis showed several independent regions of homozygosity (ROH) encompassing >12% of the genome. a) A 16‐Mb ROH on chromosome 2 (chr2:34,008,052‐50,861,049) demonstrating a copy number state of 2 and no heterozygous SNPs. The dotted vertical line denotes the location of the EPCAM gene.

Article Snippet: Sanger sequencing of the EPCAM gene was performed clinically by Prevention Genetics (Marshfield, WI).

Techniques: Microarray

Journal: Clinical Case Reports

Article Title: Identification of EPCAM mutation: clinical use of microarray

doi: 10.1002/ccr3.914

Figure Lengend Snippet: Identification of the c.1A>C variant (A) and the c.38_62 duplication (B) in the EPCAM gene.

Article Snippet: Sanger sequencing of the EPCAM gene was performed clinically by Prevention Genetics (Marshfield, WI).

Techniques: Variant Assay

Journal: Clinical Case Reports

Article Title: Identification of EPCAM mutation: clinical use of microarray

doi: 10.1002/ccr3.914

Figure Lengend Snippet: Patient's weight and height plotted on growth chart (World Health Organization). Open arrowhead: EGD performed and chromosomal microarray resulted; closed arrowhead: immunohistological analysis on tissues obtained from endoscopy showed absence of EPCAM staining; open arrow: patient placed on full TPN and enteral feeds stopped; closed arrow: DNA sequencing resulted.

Article Snippet: Sanger sequencing of the EPCAM gene was performed clinically by Prevention Genetics (Marshfield, WI).

Techniques: Microarray, Staining, DNA Sequencing