Curtis Palm's research while affiliated with Stanford University and other places

... Since the first plant genome for Arabidopsis thaliana was constructed 20 years ago [11], advances in highthroughput sequencing technology have resulted in the availability of reference genomes for over 800 land plants (https://ftp.ncbi.nlm.nih.gov/genomes/ GENOME_REPORTS/eukaryotes.txt). ...

... In complex systems that require the identification and monitoring of dozens to hundreds of microorganisms, molecular probe technology is especially useful. Molecular probe technology is a robust, culture-independent, and multiplexed means of identifying bacteria present at even low abundances (Xu et al., 2014). (A diagram of a molecular probe is shown in Fig. S1, Supplementary material.) ...

... frifolii RCAM1365 (Table 9). For example, genes nifZQXW are involved in the synthesis of the Fe-S-cofactor and fixation of molybdenum, protecting nitrogenase from the negative effects of oxygen [51,[55][56][57][58]. The fixHSQ genes play important role in the biosynthesis of the oxidase complex, which regulates the transport of oxygen through membranes, allowing normal cell breath at low oxygen concentrations [53,56]. ...

... The diameter of the cross-section of a double helix is about 20 Å [3]. But its length is up to the centimeter scale [4][5][6]. DNA is prone to forming disordered knots, which can have detrimental effects on its biological functions. ...

... Nutrient transporters may be advantageous for rhizobia, allowing them to colonize roots competitively. This may explain the large number of ABC transporters encoded in rhizobial genomes [59][60][61]. ...

... Bacterial vaginosis, described as a polybacterial dysbiosis, is a risk factor for preterm births (16)(17)(18)(19). A previous study showed that abnormal vaginal microorganisms can negatively affect the pregnancy rate among women who conceive after IVF (18), and that VMB present on the day of embryo transfer significantly affect the pregnancy outcome of IVF (live birth/no live birth) (20), indicating that some VMB might act as positive or negative biomarkers for the risk of preterm births. ...

... The second approach is to employ molecular inversion probes (MIP) carrying molecular barcodes. A good example of this approach is the single molecule Molecular Inversion Probes method [23] (Figure 1C), which combines the MIP strategy for targeted capture [32][33][34] at a single-molecule level [12,13,16,17,[21][22] . Third, molecular barcodes can also be introduced on a template by PCR amplification with target-specific primers ( Figure 1D). ...

... This approach originates from the Padlock Probes (Nilsson et al., 1994) developed further by Hardenbol et al. (2003) and they were used for large-scale human SNP genotyping (Hardenbol et al., 2005). Other applications are, for example: resequencing large sets of human exons (Turner, Lee, et al., 2009), medically relevant gene panels (O'Roak et al., 2012), detection of copy number variation (Wang et al., 2007;Ji and Welch, 2009), quantification of alternative splicing (Lin et al., 2010) or accurate genotyping of highly similar paralogs (Nuttle et al., 2013). MIPs are single-stranded DNA molecules consisting of the linker with arms containing sequences complementary to the two regions flanking the chosen target. ...

... Although the TOP1MT gene is not formally recognized as a human disease gene, our novel findings, combined with previous work by others, strengthen the argument that TOP1MT should be considered for its role in human disease. In a study of 40 patients with disorders of mtDNA maintenance, 39 candidate genes linked to mtDNA maintenance were sequenced, and two predicted pathogenic variants in TOP1MT were identified [59]. However, given the limited number of genes sequenced at the time, and a lack of mechanistic studies, a direct correlation between the patient phenotype and pathogenicity of the candidate variants was not established. ...

... A comparison between the cDNA and genomic sequences revealed four introns and five exons in the FRO1 gene. This experimentally deduced gene structure is the same as the computer-annotated version generated by the Arabidopsis Genome Initiative (Palm et al., 2000). GenBank searches found that FRO1 has high amino acid sequence similarities to the 18-kD Fe-S subunit of mitochondrial respiratory chain complex I (NADH dehydrogenase) from diverse organisms. ...