Additional file 1: of Generalizing cell segmentation and quantification

Source codes of the proposed framework with test images. (ZIP 31244 kb

High-Conductance Pathways in Ring-Strained Disilanes by Way of Direct σ‑Si–Si to Au Coordination

A highly conducting electronic contact between a strained disilane and Au is demonstrated through scanning tunneling microscope-based single-molecule measurements. Conformationally locked <i>cis</i> diastereomers of bis­(sulfide)-anchor-equipped 1,2-disilaacenaphthenes readily form high-conducting junctions in which the two sulfide anchors bind in a bipodal fashion to one gold electrode, providing enough stability for a stable electrical contact between the Si–Si σ bond and the other electrode

Partially Overlapping Primer-Based PCR for Genome Walking

<div><p>Current genome walking methods are cumbersome to perform and can result in non-specific products. Here, we demonstrate the use of partially overlapping primer-based PCR (POP-PCR), a direct genome walking technique for the isolation of unknown flanking regions. This method exploits the partially overlapping characteristic at the 3’ ends of a set of POP primers (walking primers), which guarantees that the POP primer only anneals to the POP site of the preceding PCR product at relatively low temperatures. POP primer adaptation priming at the genomic DNA/POP site occurs only once due to one low-/reduced-stringency cycle in each nested PCR, resulting in the synthesis of a pool of single-stranded DNA molecules. Of this pool, the target single-stranded DNA is replicated to the double-stranded form bound by the specific primer and the POP primer in the subsequent high-stringency cycle due to the presence of the specific primer-binding site. The non-target single stranded DNA does not become double stranded due to the absence of a binding site for any of the primers. Therefore, the POP-PCR enriches target DNA while suppressing non-target products. We successfully used POP-PCR to retrieve flanking regions bordering the <i>gadA</i> locus in <i>Lactobacillus brevis</i> NCL912, <i>malQ</i> in <i>Pichia pastoris</i> GS115, the human <i>aldolase A</i> gene, and <i>hyg</i> in rice.</p></div

Chromosome walking of the <i>gadA</i> locus of <i>Lactobacillus brevis</i> NCL912 (a), human aldolase A gene (b), <i>malQ</i> of <i>Pichia pastoris</i> GS115 (c), and <i>hyg</i> of rice (d).

<p>I: walking into 5’ regions of the genes (locus); II: walking into 3’ regions of the genes (locus). Each walking experiment contained four sets of PCRs that respectively utilized the four POP primer sets, POP1, POP2, POP3, and POP4, paired with a specific primer set. For each set of PCRs, only the results of secondary PCR (left lane) and tertiary (right lane) PCR are presented. White arrows indicate target bands. M1: DL2000 DNA marker. M2: λ-Hind III digest DNA Marker. M3: DL5000 DNA marker.</p

Aromaticity Decreases Single-Molecule Junction Conductance.

We have measured the conductance of single-molecule junctions created with three different molecular wires using the scanning tunneling microscope-based break-junction technique. Each wire contains one of three different cyclic five-membered rings: cyclopentadiene, furan, or thiophene. We find that the single-molecule conductance of these three wires correlates negatively with the resonance energy of the five-membered ring; the nonaromatic cyclopentadiene derivative has the highest conductance, while the most aromatic of this series, thiophene, has the lowest. Furthermore, we show for another wire structure that the conductance of furan-based wires is consistently higher than for analogous thiophene systems, indicating that the negative correlation between conductance and aromaticity is robust. The best conductance would be for a quinoid structure that diminishes aromaticity. The energy penalty for partly adopting the quinoid structure is less with compounds having lower initial aromatic stabilization. An additional effect may reflect the lower HOMOs of aromatic compounds

Electric Field Breakdown in Single Molecule Junctions

Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S–Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor–acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si–Si and Ge–Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si–Si, Si–C, and Si–O bonds and find that Si–C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level

Titration of substrates and cofactors.

<p>(A), Optimization of SAM concentration. The reaction mixture contained: 1 mM ALA, 200 μM NAD, 1 μM each enzyme, and various concentrations of SAM (20 μM, 50 μM, 200 μM, 500 μM, and 2 mM SAM); (B), Optimization of ALA concentration. The reaction mixture contained: 200 μM SAM, 200 μM NAD, 1 μM each enzyme, and various concentrations of ALA (0.5 mM, 1 mM, 5 mM, 20 mM, and 100 mM). Results are presented as mean ± SD. Error bars represent standard deviations of three biological replicates.</p

Analysis of variance (ANOVA) for response surface quadratic model.

<p>Analysis of variance (ANOVA) for response surface quadratic model.</p

Surface response plots showing the effects of varying PBGS, PBGD, UROS, and SUMT concentrations.

<p>(A), Effect of PBGS and PBGD concentrations. (B), Effect of PBGD and UROS concentrations. (C), Effect of UROS and SUMT concentrations. (D), Effect of PBGS and SUMT concentrations.</p

Analysis of variance (ANOVA) for reduced response surface quadratic model.

<p>Analysis of variance (ANOVA) for reduced response surface quadratic model.</p