Identifying and decoupling many-body interactions in spin ensembles in diamond

We simulate the dynamics of varying density quasi-two-dimensional spin ensembles in solid-state systems, focusing on the nitrogen-vacancy centers in diamond. We consider the effects of various control sequences on the averaged dynamics of large ensembles of spins, under a realistic "spin-bath" environment. We reveal that spin locking is efficient for decoupling spins initialized along the driving axis, both from coherent dipolar interactions and from the external spin-bath environment, when the driving is two orders of magnitude stronger than the relevant coupling energies. Since the application of standard pulsed dynamical decoupling sequences leads to strong decoupling from the environment, while other specialized pulse sequences can decouple coherent dipolar interactions, such sequences can be used to identify the dominant interaction type. Moreover, a proper combination of pulsed decoupling sequences could lead to the suppression of both interaction types, allowing additional spin manipulations. Finally, we consider the effect of finite-width pulses on these control protocols and identify improved decoupling efficiency with increased pulse duration, resulting from the interplay of dephasing and coherent dynamics

Gut microbiota dysbiosis: The potential mechanisms by which alcohol disrupts gut and brain functions

Alcohol use disorder (AUD) is a high-risk psychiatric disorder and a key cause of death and disability in individuals. In the development of AUD, there is a connection known as the microbiota-gut-brain axis, where alcohol use disrupts the gut barrier, resulting in changes in intestinal permeability as well as the gut microbiota composition, which in turn impairs brain function and worsens the patient’s mental status and gut activity. Potential mechanisms are explored by which alcohol alters gut and brain function through the effects of the gut microbiota and their metabolites on immune and inflammatory pathways. Alcohol and microbiota dysregulation regulating neurotransmitter release, including DA, 5-HT, and GABA, are also discussed. Thus, based on the above discussion, it is possible to speculate on the gut microbiota as an underlying target for the treatment of diseases associated with alcohol addiction. This review will focus more on how alcohol and gut microbiota affect the structure and function of the gut and brain, specific changes in the composition of the gut microbiota, and some measures to mitigate the changes caused by alcohol exposure. This leads to a potential intervention for alcohol addiction through fecal microbiota transplantation, which could normalize the disruption of gut microbiota after AUD

The barley pan-genome reveals the hidden legacy of mutation breeding

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding

Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize

<p>Abstract</p> <p>Background</p> <p>Auxin signaling is vital for plant growth and development, and plays important role in apical dominance, tropic response, lateral root formation, vascular differentiation, embryo patterning and shoot elongation. Auxin Response Factors (ARFs) are the transcription factors that regulate the expression of auxin responsive genes. The <it>ARF </it>genes are represented by a large multigene family in plants. The first draft of full maize genome assembly has recently been released, however, to our knowledge, the <it>ARF </it>gene family from maize (<it>ZmARF </it>genes) has not been characterized in detail.</p> <p>Results</p> <p>In this study, 31 maize (<it>Zea mays </it>L.) genes that encode ARF proteins were identified in maize genome. It was shown that maize <it>ARF </it>genes fall into related sister pairs and chromosomal mapping revealed that duplication of <it>ZmARFs </it>was associated with the chromosomal block duplications. As expected, duplication of some <it>ZmARFs </it>showed a conserved intron/exon structure, whereas some others were more divergent, suggesting the possibility of functional diversification for these genes. Out of these 31 <it>ZmARF </it>genes, 14 possess auxin-responsive element in their promoter region, among which 7 appear to show small or negligible response to exogenous auxin. The 18 <it>ZmARF </it>genes were predicted to be the potential targets of small RNAs. Transgenic analysis revealed that increased miR167 level could cause degradation of transcripts of six potential targets (<it>ZmARF3</it>, <it>9</it>, <it>16</it>, <it>18</it>, <it>22 </it>and <it>30</it>). The expressions of maize <it>ARF </it>genes are responsive to exogenous auxin treatment. Dynamic expression patterns of <it>ZmARF </it>genes were observed in different stages of embryo development.</p> <p>Conclusions</p> <p>Maize <it>ARF </it>gene family is expanded (31 genes) as compared to <it>Arabidopsis </it>(23 genes) and rice (25 genes). The expression of these genes in maize is regulated by auxin and small RNAs. Dynamic expression patterns of <it>ZmARF </it>genes in embryo at different stages were detected which suggest that maize <it>ARF </it>genes may be involved in seed development and germination.</p

Human sperm acrosome function assays are predictive of fertilization rate in vitro: a retrospective cohort study and meta-analysis

Abstract Objective To determine whether acrosome function scoring—including acrosomal enzyme (AE) levels and acrosome reaction (AR) results—can predict fertilization rate in vitro. Methods We examined the predictive value of acrosomal enzymes (AE) determined by spectrophotometry/N-α-benzoyl-dl-arginine-p-nitroanilide for fertilization rate (FR) in vitro in a retrospective cohort study of 737 infertile couples undergoing IVF therapy. Additionally, a meta-analysis was done for prospective cohort or case-control studies; the following summary measures were reported to expand upon the findings: pooled spearman correlation coefficient (Rs), standardized mean difference (SMD), sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic score (DS), diagnostic odds ratio (DOR), and area under the summary receiver operating characteristic curve (AUC). Results Lower AE levels determined by spectrophotometry with a cut-off value of   0.05). Lower AE levels determined by fluorometry or substrate assay were used for predicting lower FR with low sensitivity and high specificity; the spectrophotometry assay had an uncertain predictive value. For induced AR assay, the diagnostic performance in the other areas was inferior to that in Africa (Rs = 0.65, SMD = 1.86). No preparation or double preparation yielded inferior results as compared to one preparation (Rs = 0.41); discontinuous gradient (Rs = 0.17, SMD = 0.47) was inferior to swim up (Rs =0.65, SMD = 1.51). Nonphysiological triggers (SMD = 0.81) did not differ from physiological triggers (SMD = 0.95) in general; ZP (Rs = 0.63) or mannose (Rs = 0.59) was superior to other physiological or nonphysiological triggers; and there was no correlation for human follicle fluid, progesterone, cyclic adenosine 3′-5′-phosphate analogue and phorbol ester–BSA-GlcNAc Neoglycoproteins with N-acetylglucosamine residues. Lower induced AR% determined by indirect immunofluorescence, direct immunofluorescence with lection, or triple stain was used for predicting lower FR, with moderate sensitivity/high specificity, moderate sensitivity/high specificity, or high sensitivity/low specificity. Conclusions Although the correlation between acrosome function scoring and FR was significant, the assays were neither highly sensitive nor specific. Additionally, the diagnostic performance showed regional effects as well as an effect of the sperm preparation or assay method. More studies of multicenter, large-scale, careful design and synthesizing multiple sperm functional assays and oocyte quality assays are still needed in clinical settings to better predict fertilization outcome in IVF

miRNA164-directed cleavage of <it>ZmNAC1</it> confers lateral root development in maize (<it>Zea mays</it> L.)

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are a class of small, non-coding RNAs that regulate gene expression by binding target mRNA, which leads to cleavage or translational inhibition. The NAC proteins, which include NAM, ATAF, and CUC, are a plant-specific transcription factor family with diverse roles in development and stress regulation. It has been reported that miR164 negatively regulates <it>NAC1</it> expression, which in turn affects lateral root development in <it>Arabidopsis</it>; however, little is known about the involvement of the maize NAC family and miR164 in lateral root development.</p> <p>Results</p> <p>We collected 175 maize transcripts with NAC domains. Of these, 7 <it>ZmNACs</it> were putative targets for regulation by miR164. We isolated one gene, called <it>TC258020</it> (designated <it>ZmNAC1</it>) from 2 maize inbred lines, 87-1 and Zong3. <it>ZmNAC1</it> had a high expression level in roots and showed higher abundance (1.8 fold) in Zong3 relative to 87-1, which had less lateral roots than Zong3. There was a significant correlation between the expression level of <it>ZmNAC1</it> and the lateral root density in the recombinant inbred line (RIL) population. Transgenic <it>Arabidopsis</it> that overexpressed <it>ZmNAC1</it> had increased lateral roots in comparison to the wild type. These findings suggest that <it>ZmNAC1</it> played a significant role in lateral root development. An allelic expression assay showed that trans-regulatory elements were the dominant mediators of <it>ZmNAC1</it> differential expression in 87-1 and Zong3, and further analysis revealed that miR164 was a trans-element that guided the cleavage of endogenous <it>ZmNAC1</it> mRNA. Both mature miR164 and miR164 precursors had higher expression in 87-1 than Zong3, which was the opposite of the expression pattern of <it>ZmNAC1</it>. Additionally, the allelic assay showed that the cis-regulatory element most likely affected <it>Zm-miR164b</it>'s expression pattern. A β-glucuronidase (GUS) assay showed that the <it>Zm-miR164b</it> promoter had higher GUS activity in 87-1 than in Zong3. In addition, we detected miR164b expression in the RIL population, and the results indicated that miR164b had a higher expression level in the RILs containing 87-1 promoter than those containing Zong3 promoter.</p> <p>Conclusion</p> <p>Our results indicate one possible pathway in maize by which differences in <it>miR164b</it> promoter activity resulted in a different expression pattern for mature miR164 which negatively regulates <it>ZmNAC1</it> expression in 87-1 and Zong3, thereby contributing to a significantly different lateral root phenotype.</p

Harvesting prevascularized smooth muscle cell sheets from common polystyrene culture dishes.

Cell sheet engineering has recently emerged as a promising strategy for scaffold-free tissue engineering. However, the primary method of harvesting cell sheets using temperature-responsive dishes has potential limitations. Here we report a novel cell sheet technology based on a coculture system in which SMCs are cocultured with EPCs on common polystyrene dishes. We found that an intact and highly viable cell sheet could be harvested using mechanical methods when SMCs and EPCs were cocultured on common polystyrene dishes at a ratio of 6:1 for 5 to 6 days; the method is simple, cost-effective and highly repeatable. Moreover, the cocultured cell sheet contained capillary-like networks and could secrete a variety of angiogenic factors. Finally, in vivo studies proved that the cocultured cell sheets were more favorable for the fabrication of vascularized smooth muscle tissues compared to single SMC sheets. This study provides a promising avenue for smooth muscle tissue engineering