Center Degenerated Walking-Primer PCR: A Novel and Universal Genome-Walking Method.

Enhancing the specificity and applicability of PCR-based genome-walking methods is highly desirable. A new and universal genome-walking tool, called center degenerated walking-primer PCR (CDWP-PCR), is presented in this study. CDWP-PCR involves adopting a center degenerated walking primer (cdWP) in the secondary/tertiary round of amplification.

An RNA modification prevents extended codon-anticodon interactions from facilitating +1 frameshifting.

RNA post-transcriptional modifications act by stabilizing the functional conformations of RNA. While their role in messenger RNA (mRNA) decoding is well established, it is less clear how transfer RNA (tRNA) modifications outside the anticodon contribute to tRNA stability and accurate protein synthesis. Absence of such modifications causes translation errors, including mRNA frameshifting.

Linking molecules to metal surfaces with covalent bonds.

Covalent linkage between organic species and metal electrodes is appealing for constructing robust and highly-conducting molecular junctions. Strategies for creating covalent organic/metal contacts often involve chemical reactions, which not only offer tools for circuitry design, but also provide rich information about surface chemistry and reaction mechanism at a molecular and atomic level. This review showcases methods including transmetalation reactions employing chemical structures such as organostannanes and boronic acids, and electrochemical redox approaches using diazonium terminal groups, as well as amines and imine radicals, for forming C-Au and N-Au bonds with Au electrodes.

Uracil walking primer PCR: An accurate and efficient genome-walking tool.

Genome walking PCR has been extensively used to acquire unknown genomic regions bordering known DNAs. However, non-target amplification challenges the efficacy of existing genome-walking PCRs. Herein, we conceived a new genome-walking method termed Uracil walking Primer PCR (UP-PCR).

Arbitrarily Suffixed Sequence-Specific Primer PCR for Reliable Genome Walking: Taking Genome Walkings of brevis And Rice as Examples.

Background: Genome walking has contributed to life science-related areas. Herein, we detailed a new genome walking method, nominated as arbitrarily suffixed sequence-specific primer PCR (ASP-PCR).

Objectives: This study aimed to construct an efficient random PCR-based genome walking method.

Drying methods affected the fatty acids oxidation and bacterial community of traditional dry-cured ducks during processing and its relation with the aroma formation.

The formation of volatile compounds in dry-cured ducks produced by hot and cold air circular drying (HCAD), hot air drying (HAD), and traditional sun drying (TSD) were analyzed by E-nose and GC-MS. The HCAD exhibited higher alcohols, aldehydes, esters, and furans than that of the other two. Six, five, and three key compounds were identified by OAV in HCAD, HAD, and TSD, respectively.

Protocol to Mine Unknown Flanking DNA Using PER-PCR for Genome Walking.

Genome walking, a molecular technique for mining unknown flanking DNAs, has a wide range of uses in life sciences and related areas. Herein, a simple but reliable genome walking protocol named primer extension refractory PCR (PER-PCR) is detailed. This PER-PCR-based protocol uses a set of three walking primers (WPs): primary WP (PWP), secondary WP (SWP), and tertiary WP (TWP).

Protocol to Identify Unknown Flanking DNA Using Partially Overlapping Primer-based PCR for Genome Walking.

Genome walking is a popular molecular technique for accessing unknown flanking DNAs, which has been widely used in biology-related fields. Herein, a simple but accurate genome-walking protocol named partially overlapping primer (POP)-based PCR (POP-PCR) is described. This protocol exploits a POP set of three POPs to mediate genome walking.

Protocol to Retrieve Unknown Flanking DNA Using Fork PCR for Genome Walking.

PCR-based genome walking is one of the prevalent techniques implemented to acquire unknown flanking genomic DNAs. The worth of genome walking includes but is not limited to cloning full-length genes, mining new genes, and discovering regulatory regions of genes. Therefore, this technique has advanced molecular biology and related fields.

Protonation-Independent Charge Transport Across Diphenylamine Single-Molecule Junctions.

Amines are one of the most ubiquitous functional groups in molecular junctions; however, the exact regulation of the charge transport through the protonation state of an amine group in the junction backbone remains elusive. We address this question here by designing a diphenylamine molecular backbone and experimentally investigating how protonation of the central amine group affects the charge transport. Our ultraviolet-visible spectroscopy measurements demonstrate the protonation reaction of the diphenylamine compound in the presence of either trifluoroacetic acid or HCl, and we observe a consistent trend of a modestly increased conductance for diphenylamine in the presence of acid, indicating that a protonated amine group in a diphenylamine backbone slightly enhances the electron conduction.

Long-term effects of thinning on soil organic carbon fractions and carbon pool management indices in secondary forests of heavily burned areas.

Despite decades of recovery, soil carbon in heavily burned areas has failed to reach pre-fire levels. It is unclear whether stand management practices can promote soil organic carbon accumulation at such sites. This study evaluated the changes in soil labile organic carbon (LOC) fractions (including dissolved organic carbon (DOC), microbial biomass carbon (MBC), and easily oxidizable organic carbon (EOC)) and the carbon pool management index (CPMI) after the thinning of a heavily burned area in the Daxing'an Mountains and selected sample plots.

Method and Verification of Liquid Cooling Heat Dissipation Based on Internal Heat Source of Airborne Long-Focus Aerial Camera.

The traditional passive heat dissipation method has low heat dissipation efficiency, which is not suitable for the heat dissipation of the concentrated heat source inside the long-focal aerial camera, resulting in temperature level changes and temperature gradients in the optical system near the heat source, which seriously affect the imaging performance of the aerial camera. To solve this problem, an active heat dissipation method of liquid cooling cycle is proposed in this paper. To improve the solving efficiency and ensure simulation accuracy, a dynamic boundary information transfer method based on grid area weighting is proposed.

Uracil base PCR implemented for reliable DNA walking.

PCR-based DNA walking is of efficacy for capturing unknown flanking genomic sequences. Here, an uracil base PCR (UB-PCR) with satisfying specificity has been devised for DNA walking. Primary UB-PCR replaces thymine base with uracil base, resulting in a primary PCR product composed of U-DNAs.

Covalent Au-C Contact Formation and C-C Homocoupling Reaction from Organotin Compounds in Single-Molecule Junctions.

Formation of new chemical species has been achieved under an electric field by the use of the scanning tunneling microscope break junction technique, yet simultaneous implementation of catalytic reactions both at the organic/metal interface and in the bulk solution remains a challenging task. Herein, we show that -butyl-substituted organotin-terminated benzene undergoes both an efficient cleavage of the terminal tributyltin group to form a covalent Au-C bond and a homocoupling reaction to yield biphenyl product when subjected to an electric field in the vicinity to Au electrodes. By using ex situ characterization of high-performance liquid chromatography with an UV-vis detector, we demonstrate that the homocoupling reaction can occur with high efficiency under an extremely low tip bias voltage of ∼5 mV.

Hybrid substrate-based pH autobuffering GABA fermentation by Levilactobacillus brevis CD0817.

The probiotic fermentation of the bioactive substance gamma-aminobutyric acid (GABA) is an attractive research topic. There is still room for further improvement in reported GABA fermentation methods based on a single substrate (L-glutamic acid or L-monosodium glutamate). Here, we devised a pH auto-buffering strategy to facilitate the fermentation of GABA by Levilactobacillus brevis CD0817.

Acid-Mediated Modulation of the Conductance of Diazapentalene Molecular Junctions.

We report an acid-mediated regulation of single-molecule junction conductance achieved using an electron-deficient unit, diazapentalene, functionalized with thiophene extending units and thiomethyl aurophilic terminal groups. This diazapentalene derivative exhibits a protonation reaction in the presence of trifluoroacetic acid, as characterized by UV-vis absorption spectroscopy, and the protonated species shows a voltage-dependent single-molecule conductance, which is not observed for the pristine molecules. Specifically, under a high bias voltage of 850 mV, we observe a conductance value for the protonated molecule larger than that for the deprotonated one by a factor of 4.

N-Ended Walker PCR: An Efficient Genome-Walking Tool.

As a tool for acquiring uncharacterized genomic DNA adjacent to characterized DNA, genome-walking is integral to bioscience-related research works. Herein, a new genome-walking tool known as N-ended walker PCR (polymerase chain reaction) is presented. The key aspect for this method is the use of a degenerate walker primer in secondary/tertiary PCR.

Single primer site-specific nested PCR for accurate and rapid genome-walking.

Genome-walking is a molecular tool used to unveil uncharacterized DNA regions flanking a known DNA, which has been widely used in bioscience and related areas. This study developed a reliable and efficient PCR-based genome-walking approach, named as single primer site-specific nested PCR (SPN-PCR). A SPN-PCR set sequentially consists of three single-primer nested PCR amplifications.

Primer extension refractory PCR: an efficient and reliable genome walking method.

Genome walking, a molecular technique for obtaining unknown flanking genomic sequences from a known genomic sequence, has been broadly applied to determine transgenic sites, mine new genetic resources, and fill in chromosomal gaps. This technique has advanced genomics, genetics, and related disciplines. Here, an efficient and reliable genome walking technique, called primer extension refractory PCR (PER-PCR), is presented.

Robust binding between secondary amines and Au electrodes.

While primary amines are one of the most widely used linker groups for forming single-molecule junctions, it remains elusive whether and how the substitution of one hydrogen in a primary amine with a methyl group (secondary amine) can alter its functional properties as a linker group. Here we show that a robust binding between a secondary amine and an Au electrode is absent with the use of a non-coated Au tip and is achieved when in contact with a wax-coated Au tip, which we propose is catalyzed by the more frequent formation of Au adatoms in measurements with a wax-coated tip.

Protocol to retrieve unknown flanking DNA sequences using semi-site-specific PCR-based genome walking.

Here, we describe a protocol based on semi-site-specific primer PCR (3SP-PCR) to access unknown flanking DNA sequences. We specify the guidelines for designing primers for 3SP-PCR. We also describe experimental procedures for the 3SP-PCR, along with PCR product purification and subsequent sequencing and analysis.

Fork PCR: a universal and efficient genome-walking tool.

The reported genome-walking methods still suffer from some deficiencies, such as cumbersome experimental steps, short target amplicon, or deep background. Here, a simple and practical fork PCR was proposed for genome-walking. The fork PCR employs a fork primer set of three random oligomers to implement walking task.

Small molecule linoleic acid inhibiting whey syneresis via interact with milk proteins in the fermentation of set yogurt fortified with c9,t11-conjugated linoleic acid.

The study aimed to investigate the impact of fermentation conditions on c9,t11-conjugated linoleic acid (CLA) synthesis by Lactobacillus casei, as well as its effects on whey syneresis, water holding capacity (WHC), and texture characteristics of set yogurt. The amount of whey syneresis decreased about 30% with the adding of 0.1% linoleic acid (LA).

Sodium-Ion-Free Fermentative Production of GABA with CD0817.

Gamma-aminobutyric acid (GABA) has positive effects on many physiological processes. Lactic acid bacterial production of GABA is a future trend. This study aimed to produce a sodium-ion-free GABA fermentation process for CD0817.