Journal: bioRxiv

Article Title: Non-enzymatic assimilation of organosulfur compounds at the interface of geochemistry and biochemistry

doi: 10.64898/2026.02.18.706717

Figure Lengend Snippet: (A) The intracellular Fenton chemistry drives the ROS-driven degradation of DMSO, resulting in MSA, sulfite, CH 4 and methanol, thereby allowing for a non-enzymatic metabolic pathway of sulfur and carbon assimilation. (B) M. hispanicum respires carbon from 13 C-DMSO. Both 13 C/ 12 C ratios and formation rates of the formed CO 2 are shown, from media controls (circles) and corresponding M. hispanicum cultures (squares), from unlabeled (blue) to 13 C-labeled DMSO (red). Cartoon generated with BioRender.com .

Article Snippet: Pre-cultures of Methylobacterium hispanicum were cultivated in modified DSMZ 1629 medium, harboring 1.61 g L -1 NH4Cl, 0.2 g L -1 MgSO 4 · 7 H 2 O, 2.4 g L -1 K2HPO4, 1.1 g L -1 NaH2PO4 · 2 H2O, 4.5 mg L -1 ZnSO4 · 7 H2O, 3 mg CoCl2 · 6 H2O, 0.64 mg L -1 MnCl2 · 4 H2O, 1 mg L -1 H3BO3, 0.4 mg L -1 Na2MoO4 · 2 H2O, 0.3 mg L -1 CuSO4 · 2 H2O, and 3 mg L -1 CaCl2 · 6 H2O, which was further supplemented with 5 mL L -1 methanol, 30 mM sodium citrate and 10 mM FeCl 2 .

Techniques: Labeling, Generated

Journal: bioRxiv

Article Title: Repression of Dlx1/2 Signaling by Nolz-1/Znf503 is Essential for Parcellation of the Striatal Complex into Dorsal and Ventral Striatum

doi: 10.1101/463398

Figure Lengend Snippet: (a, c) BrdU was pulse-labeled at E12.5 and then analyzed at E18.5. Foxp1 + area was used to define the total striatal complex area (dorsal and ventral striatum). The line between the septoeminential sulcus and the piriform cortex was used to separate the dorsal from ventral striatum. The green round signals are counted as BrdU + cells (insets). BrdU E12.5 cells were decreased in dorsal Nolz-1 KO striatum. In contrast, BrdU E12.5 cells were markedly increased in the enlarged olfactory tubercle (OTe) of Nolz-1 KO ventral striatum. (b, d) Similar to the distribution of BrdU E12.5 cells, BrdU E15.5 cells were decreased in dorsal striatum, but increased in ventral striatum of Nolz-1 KO striatum. The total numbers of BrdU E12.5 cells (c) or BrdU E15.5 cells (d) are not changed in Nolz-1 KO striatum. *, p < 0.05; **, p < 0.01. n = 3/group. Scale bars in (a, b) , 200 μm.

Article Snippet: A.M. Graybiel of MIT), polyclonal goat anti-D1R antibody (1:2,000, Frontier Institute, Japan), polyclonal goat anti-D2R antibody (1:2,000, Frontier Institute, Japan), polyclonal rabbit anti-DARPP32 (1:2000; Cell Signaling), monoclonal mouse anti-Foxp1 antibody (1:1,000; kindly provided by Dr. J. Cordell of John Radcliffe Hospital, Oxford, UK), polyclonal rabbit anti-Foxp2 antibody (1:1,000; Abcam), polyclonal chicken anti-Green Fluorescent Protein (GFP; 1:1000; Abcam), polyclonal rabbit anti-Isl1 antibody (1:1,000, Abcam), monoclonal 3A4 or 4D5 mouse anti-Isl1 antibody (1:100, Developmental Studies Hybridoma Bank), monoclonal mouse anti-Ki67 (1:500 BD Pharmingen TM ), polyclonal rabbit anti-met-enkephalin antibody (1:5,000, ImmunoStar), polyclonal rabbit anti-Nolz-1 antibody (1:1,000) , monoclonal rabbit anti-Notch1 antibody (1:1,000, Abcam), polyclonal rabbit anti-Neuropilin-2 antibody (1:2,000, Cell Signaling), polyclonal goat anti-Plexin D1 antibody (1:1,000, R&D system), polyclonal rabbit anti-phospho-Histone H3 antibody (1:1,000, Millipore), monoclonal rabbit anti-Sox1 antibody (1:200; Epitomics), polyclonal rabbit anti-substance P antibody (1:3,000, Eugene Tech Inc.).

Techniques: Labeling

Journal: Environmental Microbiology

Article Title: Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates

doi: 10.1111/1462-2920.70283

Figure Lengend Snippet: (a) Maximum likelihood phylogenetic tree based on the concatenation of 120 single‐copy genes. Different colours represent different families (GTDB r220). The tree scale bar represents 0.1 substitutions per site. The numbers in nodes represent bootstrap values, and accession numbers are given in parentheses. Thermoanaerobacter kivui was used as an outgroup and root of the tree. (b) Average nucleotide identity comparisons between publicly available Thermincola strains and strain AZ34E. (c) Average nucleotide identity comparisons between publicly available Carboxydocella strains and strain AZ29I.

Article Snippet: In addition, DNA from a growing culture of Thermincola carboxydiphila (DSM 17129 T ) was obtained from the German Collection of Microorganisms and Cell Culture (DSMZ, Braunschweig, Germany).

Techniques:

Journal: Environmental Microbiology

Article Title: Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates

doi: 10.1111/1462-2920.70283

Figure Lengend Snippet: Bubble plot depicting the completeness of selected KEGG modules in Thermincola and Carboxydocella genomes. Different colours represent different genomes. The size of the bubbles corresponds to different KEGG modules' completeness values.

Article Snippet: In addition, DNA from a growing culture of Thermincola carboxydiphila (DSM 17129 T ) was obtained from the German Collection of Microorganisms and Cell Culture (DSMZ, Braunschweig, Germany).

Techniques:

Journal: Environmental Microbiology

Article Title: Comparative Physiology and Genomics of Thermincola and Carboxydocella Strains and Description of Two Novel Isolates

doi: 10.1111/1462-2920.70283

Figure Lengend Snippet: Phylogenetic comparison of CODHs detected in the Themincola and Carboxydocella genomes. The tree was constructed with the LG + G4 model in IQ‐TREE v2.0.6 and visualised in iTOL v6.8.1. CODH sequences of Thermincola sp. strain AZ34E and Carboxydocella sp. strain AZ29I are depicted in bold. The CODHs of Carboxydothermus hydrogenoformans were used as reference points for functional predictions. The tree scale bar represents 1 substitution per site. The circles in nodes represent bootstrap values > 80. The genomic structure of cooS gene clusters encoding the different CODHs in Thermincola sp. strain AZ34E and Carboxydocella sp. strain AZ291 are shown in the boxes on the top right corner. Gene abbreviations: acsB, Acetyl‐CoA synthase; acsC, corrinoid iron–sulfur protein large subunit; acsD, corrinoid iron–sulfur protein small subunit; acsE, methyltransferase A; ATPase, AAA family ATPase; cooA, CO‐dependent transcriptional activator; cooC, CODH chaperone; cooF, ferredoxin‐like electron transfer Fe‐S protein; cooMKLXUH, sub‐units of the energy‐converting hydrogenase; cooS, CO‐dehydrogenase; FNOR, NAD/FAD oxidoreductase; hp, hypothetical protein; hypA, hydrogenase maturation protein; nqrF, Na(+)‐translocating NADH‐quinone reductase subunit F; TR, transcription regulator; YlmC, YlmC/YmxH family sporulation protein; YpiB, YpiB family protein.

Article Snippet: In addition, DNA from a growing culture of Thermincola carboxydiphila (DSM 17129 T ) was obtained from the German Collection of Microorganisms and Cell Culture (DSMZ, Braunschweig, Germany).

Techniques: Comparison, Construct, Functional Assay