Spectrum structures and biological functions of 8-mers in the human genome

The spectra of k-mer frequencies can reveal the structures and evolution of genome sequences. We confirmed that the trimodal spectrum of 8-mers in human genome sequences is distinguished only by CG2, CG1 and CG0 8-mer sets, containing 2,1 or 0 CpG, respectively. This phenomenon is called independent selection law. The three types of CG 8-mers were considered as different functional elements. We conjectured that (1) nucleosome binding motifs are mainly characterized by CG1 8-mers and (2) the core structural units of CpG island sequences are predominantly characterized by CG2 8-mers. To validate our conjectures, nucleosome occupied sequences and CGI sequences were extracted, then the sequence parameters were constructed through the information of the three CG 8-mer sets respectively. ROC analysis showed that CG1 8-mers are more preference in nucleosome occupied segments (AUC > 0.7) and CG2 8-mers are more preference in CGI sequences (AUC > 0.99). This validates our conjecture in principle.     

Absorption of the flavin dimers

The electronic absorption spectra of the flavomononucleotide (FMN) in aqueous solution and in glycerine-water solution with change of the dye concentration have been measured. The FMN dimer absorption spectrum, monomer absorption spectrum, dimerization constant K and molar fraction of the monomer were calculated. It was found that FMN dimerization constants in aqueous solution were K_a = 118.0 l/mol and in glycerine K_g = 20.5 l/mol. In the region of the monomer absorption band two dimer absorption bands appear, in accordance with the Kasha molecular exciton theory.     

An X-ray spectrum estimation method from transmission measurement combined with scatter correction

PurposeConventional x-ray spectrum estimation methods from transmission measurement often lead to inaccurate results when extensive x-ray scatter is present in the measured projection. This study aims to apply the weighted L1-norm scatter correction algorithm in spectrum estimation for reducing residual differences between the estimated and true spectrum.MethodThe scatter correction algorithm is based on a simple radiographic scattering model where the intensity of scattered x-ray is directly estimated from a transmission measurement. Then, the scatter-corrected measurement is used for the spectrum estimation method that consists of deciding the weights of predefined spectra and representing the spectrum as a linear combination of the predefined spectra with the weights. The performances of the estimation method combined with scatter correction are evaluated on both simulated and experimental data.ResultsThe results show that the estimated spectra using the scatter-corrected projection nearly match the true spectra. The normalized-root-mean-square-error and the mean energy difference between the estimated spectra and corresponding true spectra are reduced from 5.8% and 1.33 keV without the scatter correction to 3.2% and 0.73 keV with the scatter correction for both simulation and experimental data, respectively.ConclusionsThe proposed method is more accurate for the acquisition of x-ray spectrum than the estimation method without scatter correction and the spectrum can be successfully estimated even the materials of the filters and their thicknesses are unknown. The proposed method has the potential to be used in several diagnostic x-ray imaging applications.     

Trace elements in children with autism spectrum disorder: A meta-analysis based on case-control studies

Autism spectrum disorder (ASD) is a common childhood neurodevelopmental disorder that may be related to trace elements. However, reports on the relationship between them are still inconsistent. In this article, we conducted a meta-analysis on this issue. We searched the PubMed, EMBASE, and Cochrane databases as of November 15, 2019. A random-effects model was used, and subgroups of studies were analyzed using samples of different measurements. Twenty-two original articles were identified (18 trace elements, including a total of 1014 children with ASD and 999 healthy controls). In autistic children, the overall levels of barium (Ba), mercury (Hg), lithium (Li), and lead (Pb) were higher. There were significant differences in the levels of copper (Cu) in the hair and serum between autistic children and the control group. The levels of Hg, Li, Pb and selenium (Se) in the hair of autistic children were higher than those of healthy children, while the levels of zinc (Zn) in the blood were lower. Excessive exposure to toxic heavy metals and inadequate intake of essential metal elements may be associated with ASD. Preventing excessive exposure to toxic metals and correcting poor dietary behaviors may be beneficial for the prevention and treatment of the disease.     

Diminished social interaction incentive contributes to social deficits in mouse models of autism spectrum disorder

One of the core symptoms of autism spectrum disorder (ASD) is impaired social interaction. Currently, no pharmacotherapies exist for this symptom due to complex biological underpinnings and distinct genetic models which fail to represent the broad disease spectrum. One convincing hypothesis explaining social deficits in human ASD patients is amotivation, however it is unknown whether mouse models of ASD represent this condition. Here we used two highly trusted ASD mouse models (male Shank3‐deficient [Shank3^+/ΔC] mice modeling the monogenic etiology of ASD, and inbred BTBR mice [both male and female] modeling the idiopathic and highly polygenic pathology for ASD) to evaluate the level of motivation to engage in a social interaction. In the behavioral paradigms utilized, a social stimulus was placed in the open arm of the elevated plus maze (EPM), or the light compartment of the light‐dark box (LDB). To engage in a social interaction, mice were thus required to endure innately aversive conditions (open areas, height, and/or light). In the modified EPM paradigm, both Shank3^+/ΔC and BTBR mice demonstrated decreased open‐arm engagement with a social stimulus but not a novel object, suggesting reduced incentive to engage in a social interaction in these models. However, these deficits were not expressed under the less severe aversive pressures of the LDB. Collectively, we show that ASD mouse models exhibit diminished social interaction incentive, and provide a new investigation strategy facilitating the study of the neurobiological mechanisms underlying social reward and motivation deficits in neuropsychiatric disorders.     

柑橘木虱成虫趋光行为反应

柑橘木虱Diaphorina citri Kuwayama是柑橘黄龙病(huanglongbing,HLB)的重要传播媒介。为了利用灯光诱控技术防治柑橘木虱,本实验于室内条件下研究柑橘木虱对波长为360 nm、400 nm、440 nm、480 nm、520 nm、560 nm和600 nm的LED光源和不同光照强度趋光行为反应。结果表明:柑橘木虱对7种单色光都有正趋向性。其中雌雄混合存在时对400 nm的紫光趋向性最强,其次是560 nm的绿光;单独处理时,雌成虫对400 nm的紫光趋性最强,其次是520 nm的绿光,雄成虫则是对520 nm的绿光趋性最强,其次是400 nm的紫光。在200μw/cm 2到1000μw/cm 2的光照强度范围内,随着光照强度的增大,柑橘木虱雄成虫趋光行为逐渐增强,在光照强度为1000μw/cm 2时趋光行为最强,但雌成虫趋光行为变化不明显。该研究表明:柑橘木虱雌雄成虫具有明显的正趋光性,且对光谱和光强的反应存在差异。这一结果可为柑橘木虱田间的灯光诱控提供实验依据。     

Muscle endurance time estimation during isometric training using electromyogram and supervised learning

Constant-force isometric muscle training is useful for increasing the maximal strength , rehabilitation and work-fatigue assessment. Earlier studies have shown that muscle fatigue characteristics can be used for evaluating muscle endurance limit. Study Objective: To predict muscle endurance time during isometric task using frequency spectrum characteristics of surface electromyography signals along with analysis of frequency spectrum shape and scale during fatigue accumulation. Method: Thirteen subjects performed isometric lateral raise at 60% MVC of deltoid (lateral) till endurance limit. Time windowed sEMG frequency spectrum was modelled using 2-parameter distributions namely Gamma and Weibull for spectrum analysis and endurance prediction. Results: Gamma distribution provided better spectrum fitting (P < 0.001) than Weibull distribution. Spectrum Distribution demonstrated no change in shape but shifted towards lower frequency with increase of magnitude at characteristic mode frequency. Support Vector Regression based algorithm was developed for endurance time estimation using features derived from fitted frequency spectrum. Time taken till endurance limit for acquired dataset 38.53 ± 17.33 s (Mean ± Standard Deviation) was predicted with error of 0.029 ± 4.19 s . R-square: 0.956, training and test sets RMSE was calculated as 3.96 and 4.29 s respectively. The application of the algorithm suggested that model required 70% of sEMG signal from maximum time of endurance for high prediction accuracy. Conclusion: Endurance Limit prediction algorithm was developed for quantification of endurance time for optimizing isometric training and rehabilitation. Our method could help personalize and change conventional training method of same weight and duration for all subjects with optimized training parameters, based upon individual sEMG activity.     

Incorporation of β‐amino acids into ascidiacyclamides: Effects on conformation,cytotoxicity and interaction with copper (II) ion

Seven ascidiacyclamide [cyclo(–Ile–oxazoline–d ‐Val–thiazole–)₂] (ASC) analogues incorporating the β‐amino acids βIle, βoxazoline, and/or d ‐βVal were synthesized. We then investigated the effects of the position and number of incorporated β‐amino acids on the structure, cytotoxicity, and copper binding by these seven analogues. The structural analyses revealed that both βIle and d ‐βVal favor a gauche‐type θ torsion angles, while βoxazoline favors a trans‐type θ torsion angle. Expansion of the macrocycle by incorporation of βIle or d ‐βVal readily induced molecular folding. On the other hand, the incorporation of two βoxazoline residues strongly extended the peptide conformation, and the incorporation of one was sufficient for the moderate restriction important for conformational equilibrium and cytotoxicity. Despite expansion of the macrocycles, the structure‐cytotoxicity relationships were largely maintained. In studies of complexation of the analogues with Cu (II) ion, the position and number of incorporated β‐amino acids had a large impact on the structure of the metal complex and may contribute to its stabilization.     

Human exploitation shapes productivity–biomass relationships on coral reefs

Coral reef fisheries support the livelihoods of millions of people in tropical countries, despite large‐scale depletion of fish biomass. While human adaptability can help to explain the resistance of fisheries to biomass depletion, compensatory ecological mechanisms may also be involved. If this is the case, high productivity should coexist with low biomass under relatively high exploitation. Here we integrate large spatial scale empirical data analysis and a theory‐driven modelling approach to unveil the effects of human exploitation on reef fish productivity–biomass relationships. We show that differences in how productivity and biomass respond to overexploitation can decouple their relationship. As size‐selective exploitation depletes fish biomass, it triggers increased production per unit biomass, averting immediate productivity collapse in both the modelling and the empirical systems. This ‘buffering productivity’ exposes the danger of assuming resource production–biomass equivalence, but may help to explain why some biomass‐depleted fish assemblages still provide ecosystem goods under continued global fishing exploitation.     

MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non‐Modified Peptides

A large number of post‐translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot‐gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non‐modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools will preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, MMS2plot, an R package for visualizing peptide‐spectrum matches (PSMs) for multiple peptides, is described. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. MMS2plot is expected to play an important role in PTM discovery from large‐scale proteomics datasets generated by liquid chromatography‐MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL‐3 license.