On the Origin of Western Diet Pathologies

The ratio of the two sulfur-containing amino acids, methionine (Met) and cysteine (Cys), may be a determining factor for which foods contribute to longevity and health. It is shown here that substantially more Met than Cys is consistently found in foods, such as dairy and meat products, thought to contribute to pathologies associated with the Western Diet

A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

As the scope of microbial surveys expands with the parallel growth in sequencing capacity, a significant bottleneck in data analysis is the ability to generate a biologically meaningful multiple sequence alignment. The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm. The purpose of this study was to create and validate an aligner with the goal of quickly generating a high quality alignment and having the flexibility to use any reference alignment. Using the simple nearest alignment space termination algorithm, the resulting aligner operates in linear time, requires a small memory footprint, and generates a high quality alignment. In addition, the alignments generated for variable regions were of as high a quality as the alignment of full-length sequences. As implemented, the method was able to align 18 full-length 16S rRNA gene sequences and 58 V2 region sequences per second to the 50,000-column SILVA reference alignment. Most importantly, the resulting alignments were of a quality equal to SILVA-generated alignments. The aligner described in this study will enable scientists to rapidly generate robust multiple sequences alignments that are implicitly based upon the predicted secondary structure of the 16S rRNA molecule. Furthermore, because the implementation is not connected to a specific database it is easy to generalize the method to reference alignments for any DNA sequence

A Survey of Oxidative Paracatalytic Reactions Catalyzed by Enzymes That Generate Carbanionic Intermediates: Implications for ROS Production, Cancer Etiology, and Neurodegenerative Diseases

Enzymes that generate carbanionic intermediates often catalyze paracatalytic reactions with O2 and other electrophiles not considered “normal” reactants. For example, pyridoxal 5′-phosphate (PLP)—containing pig kidney dopa decarboxylase oxidizes dopamine with molecular O2 to 3,4-dihydroxyphenylacetaldehyde at about 1% of the rate at which it catalyzes nonoxidative dopa decarboxylation. The mutant Y332F enzyme, however, catalyzes stoichiometric conversion of dopa to 3,4-dihydroxyphenylacetaldehyde, suggesting that even minor structural changes may alter or initiate paracatalytic reactions catalyzed by certain enzymes. Carbanions generated by several thiamine diphosphate (ThDP)—dependent enzymes react with different electrophiles, transforming some xenobiotics and endogenous compounds into potentially biologically hazardous products. The detrimental effects of paracatalytic reactions may be greatly increased by cellular compartmentation of enzymes and intermediates. For example, in two of the the three multienzyme complexes involved in oxidative α-keto acid decarboxylation, paracatalytic reactions of the third component inactivate the first carbanion-generating component. In this review we provide an outline of carbanion-generating enzymes known to catalyze paracatalytic reactions. We also discuss the potential of some of these reactions to contribute to irreversible damage in cancer and neurodegeneration through disease-induced alterations in the metabolic state and/or protein structure

Simultaneous Broadband Vector Magnetometry Using Solid-State Spins

We demonstrate a vector magnetometer that simultaneously measures all Cartesian components of a dynamic magnetic field using an ensemble of nitrogen-vacancy (NV) centers in a single-crystal diamond. Optical NV-diamond measurements provide high-sensitivity, broadband magnetometry under ambient or extreme physical conditions; and the fixed crystallographic axes inherent to this solid-state system enable vector sensing free from heading errors. In the present device, multi-channel lock-in detection extracts the magnetic-field-dependent spin resonance shifts of NVs oriented along all four tetrahedral diamond axes from the optical signal measured on a single detector. The sensor operates from near DC up to a $12.5$ kHz measurement bandwidth; and simultaneously achieves $\sim\!50$ pT/$\sqrt{\text{Hz}}$ magnetic field sensitivity for each Cartesian component, which is to date the highest demonstrated sensitivity of a full vector magnetometer employing solid-state spins. Compared to optimized devices interrogating the four NV orientations sequentially, the simultaneous vector magnetometer enables a $4\times$ measurement speedup. This technique can be extended to pulsed-type sensing protocols and parallel wide-field magnetic imaging.Comment: 13 pages, 5 figures, 1 table, Supplemental Material included as ancillary fil

Sensitivity Optimization for NV-Diamond Magnetometry

Solid-state spin systems including nitrogen-vacancy (NV) centers in diamond constitute an increasingly favored quantum sensing platform. However, present NV ensemble devices exhibit sensitivities orders of magnitude away from theoretical limits. The sensitivity shortfall both handicaps existing implementations and curtails the envisioned application space. This review analyzes present and proposed approaches to enhance the sensitivity of broadband ensemble-NV-diamond magnetometers. Improvements to the spin dephasing time, the readout fidelity, and the host diamond material properties are identified as the most promising avenues and are investigated extensively. Our analysis of sensitivity optimization establishes a foundation to stimulate development of new techniques for enhancing solid-state sensor performance.Comment: 73 pages, 36 figures, 17 table

Ultralong Dephasing Times in Solid-State Spin Ensembles via Quantum Control

Quantum spin dephasing is caused by inhomogeneous coupling to the environment, with resulting limits to the measurement time and precision of spin-based sensors. The effects of spin dephasing can be especially pernicious for dense ensembles of electronic spins in the solid-state, such as for nitrogen-vacancy (NV) color centers in diamond. We report the use of two complementary techniques, spin bath control and double quantum coherence, to enhance the inhomogeneous spin dephasing time ($T_2^*$) for NV ensembles by more than an order of magnitude. In combination, these quantum control techniques (i) eliminate the effects of the dominant NV spin ensemble dephasing mechanisms, including crystal strain gradients and dipolar interactions with paramagnetic bath spins, and (ii) increase the effective NV gyromagnetic ratio by a factor of two. Applied independently, spin bath control and double quantum coherence elucidate the sources of spin dephasing over a wide range of NV and spin bath concentrations. These results demonstrate the longest reported $T_2^*$ in a solid-state electronic spin ensemble at room temperature, and outline a path towards NV-diamond magnetometers with broadband femtotesla sensitivity.Comment: PRX versio

Quantum Diamond Microscope for Dynamic Imaging of Magnetic Fields

Wide-field imaging of magnetic signals using ensembles of nitrogen-vacancy (NV) centers in diamond has garnered increasing interest due to its combination of micron-scale resolution, millimeter-scale field of view, and compatibility with diverse samples from across the physical and life sciences. Recently, wide-field NV magnetic imaging based on the Ramsey protocol has achieved uniform and enhanced sensitivity compared to conventional measurements. Here, we integrate the Ramsey-based protocol with spin-bath driving to extend the NV spin dephasing time and improve magnetic sensitivity. We also employ a high-speed camera to enable dynamic wide-field magnetic imaging. We benchmark the utility of this quantum diamond microscope (QDM) by imaging magnetic fields produced from a fabricated wire phantom. Over a $270\times270 \hspace{0.08333em} \mu\mathrm{m}$$^2$ field of view, a median per-pixel magnetic sensitivity of $4.1(1)\hspace{0.08333em}\mathrm{nT}$$/\sqrt{\mathrm{Hz}}$ is realized with a spatial resolution $\lesssim\hspace{0.08333em}10\hspace{0.08333em}\mu\mathrm{m}$ and sub-millisecond temporal resolution. Importantly, the spatial magnetic noise floor can be reduced to the picotesla scale by time-averaging and signal modulation, which enables imaging of a magnetic-field pattern with a peak-to-peak amplitude difference of about $300\hspace{0.08333em}\mathrm{pT}$. Finally, we discuss potential new applications of this dynamic QDM in studying biomineralization and electrically-active cells.Comment: 18 Pages, 13 figure