Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

Abstract Background Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the knowledge provided by the new sequencing technologies. Results We propose here a computational method for optimizing the choice of primer sets, based on multi-objective optimization, which simultaneously: 1) maximizes efficiency and specificity of target amplification; 2) maximizes the number of different bacterial 16S sequences matched by at least one primer; 3) minimizes the differences in the number of primers matching each bacterial 16S sequence. Our algorithm can be applied to any desired amplicon length without affecting computational performance. The source code of the developed algorithm is released as the mopo16S software tool (Multi-Objective Primer Optimization for 16S experiments) under the GNU General Public License and is available at http://sysbiobig.dei.unipd.it/?q=Software#mopo16S. Conclusions Results show that our strategy is able to find better primer pairs than the ones available in the literature according to all three optimization criteria. We also experimentally validated three of the primer pairs identified by our method on multiple bacterial species, belonging to different genera and phyla. Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by primers

24 mJ Cr+4:forsterite four-stage master-oscillator power-amplifier laser system for high resolution mid-infrared spectroscopy

We present the design of a Cr:forsterite based single-frequency master-oscillator power-amplifier laser system delivering much higher output energy compared to previous literature reports. The system has four amplifying stages with two-pass configuration each, thus enabling the generation of 24 mJ output energy in the spectral region around 1262 nm. It is demonstrated that the presented Cr:forsterite amplifier preserves high spectral and pulse quality, allowing a straightforward energy scaling. This laser system is a promising tool for tunable nonlinear down-conversion to the mid-infrared spectral range and will be a key building block in a system for high-resolution muonic hydrogen spectroscopy in the 6.8 \u3bcm rang

The experimental setup of FAMU to measure the proton Zemach radius

The FAMU experiment data acquisition is approaching. During September 2022 the full experimental setup is going to measure for the first time the muonic hydrogen ground state hyperfine splitting and obtain a precise measurement of the proton Zemach radius, shedding some new light on the proton radius puzzle. This result will not be possible without a complete system which joins nuclear and laser physics. The FAMU setup is formed by a gas cryogenic target filled with a mixture of hydrogen and oxygen in which muons injected from the RIKEN-RAL facility (UK) are stopped. The muonic hydrogen produced is then exposed to a tunable infrared laser beam, unique for its energy and narrow linewidth, able to induce the hyperfine energy jump. The transition will be measured as a variation of the muonic transfer rate from hydrogen to oxygen, observed through the detection of the X-rays emitted during the de-exitation of muonic oxygen. This presentation will describe the final setup which is being installed in all its parts

Development of the FAMU experimental apparatus for the proton radius measurement

The proton, the nucleus of the hydrogen atom, is the building block of the universe and its fascinating internal structure is defined by Quantum Chromo-Dynamics. Our experiment will measure the hyperfine splitting of the muonic hydrogen atom (μp) to study the proton’s internal magnetic structure by laser exciting from singlet μp to the triplet state with an original technique that we have proposed and tested in recent years. Have had the chance to enter the FAMU (Fisica degli Atomi MUonici) experiment in its final realization phase and I could take part in the development of all aspects of the experiment from the preliminary data taking and the subsequent analysis to the definition of the layout and the development of the laser. In particular, I took part in the preliminary data collection at ISIS accelerator facility at Rutherford Appleton Laboratory (RAL) in UK. I contributed to the analysis of the data collected by the detectors based on Ce:LaBr3 scintillation crystals with an innovative readout based on SiPM (Silicon Photo-Multiplier), finding useful improvements to perfection the resolution of these detectors. I also analyzed the data collected in the 2016 FAMU data acquisition, improving the knowledge on the argon transfer rate dependence on the temperature and X-rays de-excitation energy spectra. I designed the trigger system and realized the laser data acquisition system. The major work in which I was involved was on FAMU laser system, which will excite the hyperfine splitting transition, the most crucial part of the experiment. I participated, taking also the responsibility of the laser safety officer a RAL, to the development and characterization of the oscillator and amplifier for the 1.26 μm laser source, which we developed on purpose for our experiment. The test and qualification of all the non-linear crystals were additional aspects of my work for our laser source, for which I developed the whole laser control program. This program allows to control remotely and in real time every aspect of the laser: from the wavelength to the energy production and the control of the stabilization of the beams through a feedback system developed on purpose. Hit by the consequences of the COVID-19 pandemic, while continuously improving the laser and experiment layout, we were forced to postpone the data acquisition of the experiment at RAL in September 2022, after the one-year-long maintenance shutdown of the accelerator.The proton, the nucleus of the hydrogen atom, is the building block of the universe and its fascinating internal structure is defined by Quantum Chromo-Dynamics. Our experiment will measure the hyperfine splitting of the muonic hydrogen atom (μp) to study the proton’s internal magnetic structure by laser exciting from singlet μp to the triplet state with an original technique that we have proposed and tested in recent years. Have had the chance to enter the FAMU (Fisica degli Atomi MUonici) experiment in its final realization phase and I could take part in the development of all aspects of the experiment from the preliminary data taking and the subsequent analysis to the definition of the layout and the development of the laser. In particular, I took part in the preliminary data collection at ISIS accelerator facility at Rutherford Appleton Laboratory (RAL) in UK. I contributed to the analysis of the data collected by the detectors based on Ce:LaBr3 scintillation crystals with an innovative readout based on SiPM (Silicon Photo-Multiplier), finding useful improvements to perfection the resolution of these detectors. I also analyzed the data collected in the 2016 FAMU data acquisition, improving the knowledge on the argon transfer rate dependence on the temperature and X-rays de-excitation energy spectra. I designed the trigger system and realized the laser data acquisition system. The major work in which I was involved was on FAMU laser system, which will excite the hyperfine splitting transition, the most crucial part of the experiment. I participated, taking also the responsibility of the laser safety officer a RAL, to the development and characterization of the oscillator and amplifier for the 1.26 μm laser source, which we developed on purpose for our experiment. The test and qualification of all the non-linear crystals were additional aspects of my work for our laser source, for which I developed the whole laser control program. This program allows to control remotely and in real time every aspect of the laser: from the wavelength to the energy production and the control of the stabilization of the beams through a feedback system developed on purpose. Hit by the consequences of the COVID-19 pandemic, while continuously improving the laser and experiment layout, we were forced to postpone the data acquisition of the experiment at RAL in September 2022, after the one-year-long maintenance shutdown of the accelerator

FAMU experiment: measurement of the transfer rate from up to oxygen

The main goal of the FAMU experiment is to measure for the first time the hyperfine splitting of the muonic hydrogen ground state and, through this measurement, to determine the proton Zemach radius. To achieve this result, it is necessary to characterize first the muon transfer mechanism from muonic hydrogen to oxygen. This study has been carried on by the FAMU Collaboration at the RIKEN-RAL muon facility in the UK. In this work the most recent results on this topic are presented

The optimal hybrid/electric ferry for the Liguria Natural Parks

With this work we want to contribute to the evaluation of the effectiveness of using an electric/hybrid Ferry boat for tourist transportation in a real case. For this purpose, it is necessary to define the \u201coptimal\u201d systems configuration of the Ferry boat in term of engine power, energy storage and photovoltaic system sizes and also percentage of hybrid or pure electric usage. However the adjective \u201coptimal\u201d cannot have an absolute definition because it strongly depends on the context we are evaluating the problem and also subjective factors, not easily quantifiable, enter the evaluation of optimal system. For example, for a ferry working in marine Natural Parks like those around La Spezia harbor, operating and initial costs are important parameters to be considered, but pollution, noise and comfort are at least as much important ones. Moreover, due to the constraints given by the battery storage system (volume, weight, cost and recharge time) the hybrid/electric system of the ferry must be well targeted at the specific routes and possible stages in the transport service around the La Spezia Gulf. For that reason, we focus to the determination of an optimal hybrid ferryboat, aimed at the specific case of La Spezia. We think that the analysis here performed can be replicated to other cases and may be useful in showing the potential of these new technologies for a more sustainable boating, both from the environmental and economic point of view, while also improving the service provided to passengers, especially in terms of comfort