Validity of single-channel model for a spin-orbit coupled atomic Fermi gas near Feshbach resonances

We theoretically investigate a Rashba spin-orbit coupled Fermi gas near Feshbach resonances, by using mean-field theory and a two-channel model that takes into account explicitly Feshbach molecules in the close channel. In the absence of spin-orbit coupling, when the channel coupling $g$ between the closed and open channels is strong, it is widely accepted that the two-channel model is equivalent to a single-channel model that excludes Feshbach molecules. This is the so-called broad resonance limit, which is well-satisfied by ultracold atomic Fermi gases of $^{6}$Li atoms and $^{40}$K atoms in current experiments. Here, with Rashba spin-orbit coupling we find that the condition for equivalence becomes much more stringent. As a result, the single-channel model may already be insufficient to describe properly an atomic Fermi gas of $^{40}$K atoms at a moderate spin-orbit coupling. We determine a characteristic channel coupling strength $g_{c}$ as a function of the spin-orbit coupling strength, above which the single-channel and two-channel models are approximately equivalent. We also find that for narrow resonance with small channel coupling, the pairing gap and molecular fraction is strongly suppressed by SO coupling. Our results can be readily tested in $^{40}$K atoms by using optical molecular spectroscopy.Comment: 6 pages, 6 figure

MicroRNA-like RNAs from the same miRNA precursors play a role in cassava chilling responses

Abstract MicroRNAs (miRNAs) are known to play important roles in various cellular processes and stress responses. MiRNAs can be identified by analyzing reads from high-throughput deep sequencing. The reads realigned to miRNA precursors besides canonical miRNAs were initially considered as sequencing noise and ignored from further analysis. Here we reported a small-RNA species of phased and half-phased miRNA-like RNAs different from canonical miRNAs from cassava miRNA precursors detected under four distinct chilling conditions. They can form abundant multiple small RNAs arranged along precursors in a tandem and phased or half-phased fashion. Some of these miRNA-like RNAs were experimentally confirmed by re-amplification and re-sequencing, and have a similar qRT-PCR detection ratio as their cognate canonical miRNAs. The target genes of those phased and half-phased miRNA-like RNAs function in process of cell growth metabolism and play roles in protein kinase. Half-phased miR171d.3 was confirmed to have cleavage activities on its target gene P-glycoprotein 11, a broad substrate efflux pump across cellular membranes, which is thought to provide protection for tropical cassava during sharp temperature decease. Our results showed that the RNAs from miRNA precursors are miRNA-like small RNAs that are viable negative gene regulators and may have potential functions in cassava chilling responses

Synthesis and structure of the inclusion complex {NdQ[5]K@Q[10](H₂O)4}·4NO₃·20H₂O

Heating a mixture of Nd(NO₃)₃·6H₂O, KCl, Q[10] and Q[5] in HCl for 10 min affords the inclusion complex {NdQ[5]K@Q[10](H₂O)₄}·4NO₃·20H₂O. The structure of the inclusion complex has been investigated by single crystal X-ray diffraction and by X-ray Photoelectron spectroscopy (XPS)

Potential functions of microRNAs in starch metabolism and development revealed by miRNA transcriptome profiling of cassava cultivars and their wild progenitor

BACKGROUND: MicroRNAs (miRNAs) are small (approximately 21 nucleotide) non-coding RNAs that are key post-transcriptional gene regulators in eukaryotic organisms. More than 100 cassava miRNAs have been identified in a conservation analysis and a repertoire of cassava miRNAs have also been characterised by next-generation sequencing (NGS) in recent studies. Here, using NGS, we profiled small non-coding RNAs and mRNA genes in two cassava cultivars and their wild progenitor to identify and characterise miRNAs that are potentially involved in plant growth and starch biosynthesis. RESULTS: Six small RNA and six mRNA libraries from leaves and roots of the two cultivars, KU50 and Arg7, and their wild progenitor, W14, were subjected to NGS. Analysis of the sequencing data revealed 29 conserved miRNA families and 33 new miRNA families. Together, these miRNAs potentially targeted a total of 360 putative target genes. Whereas 16 miRNA families were highly expressed in cultivar leaves, another 13 miRNA families were highly expressed in storage roots of cultivars. Co-expression analysis revealed that the expression level of some targets had negative relationship with their corresponding miRNAs in storage roots and leaves; these targets included MYB33, ARF10, GRF1, RD19, APL2, NF-YA3 and SPL2, which are known to be involved in plant development, starch biosynthesis and response to environmental stimuli. CONCLUSION: The identified miRNAs, target mRNAs and target gene ontology annotation all shed light on the possible functions of miRNAs in Manihot species. The differential expression of miRNAs between cultivars and their wild progenitor, together with our analysis of GO annotation and confirmation of miRNA: target pairs, might provide insight into know the differences between wild progenitor and cultivated cassava. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-014-0355-7) contains supplementary material, which is available to authorized users

PAV markers in <i>Sorghum bicolour</i>:genome pattern, affected genes and pathways, and genetic linkage map construction

KEY MESSAGE: 5,511 genic small-size PAVs in sorghum were identified and examined, including the pattern and the function enrichment of PAV genes. 325 PAV markers were developed to construct a genetic map. ABSTRACT: Presence/absence variants (PAVs) correlate closely to the phenotypic variation, by impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and the possibility of using them as molecular markers, we generated next generation genome sequencing data for four sorghum inbred lines and used associated bioinformatic pipelines to identify small-size PAVs (40–10 kb). Five thousand five hundreds and eleven genic PAVs (40–10 kb) were identified and found to affect 3,238 genes. These PAVs were mainly distributed on the sub-telomeric regions, but the highest proportions occurred in the vicinity of the centromeric regions. One of the prominent features of the PAVs is the high occurrence of long terminal repeats retrotransposons and DNA transposons. PAVs caused various alterations to gene structure, primarily including the coding sequence variants, intron variants, transcript ablation, and initiator codon changes. The genes affected by PAVs were significantly enriched in those involved in stress responses and protein modification. We used 325 PAVs polymorphic between two sorghum inbred lines Ji2731 and E-Tian, together with 49 SSR markers, and constructed a genetic map, which consisted of 10 linkage groups corresponding to the 10 chromosomes of sorghum and spanned 1,430.3 cM in length covering 97 % of the physical genome. The resources reported here should be useful for genetic study and breeding of sorghum and related species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-015-2458-4) contains supplementary material, which is available to authorized users

Dimethyl 3,3′-diphenyl-2,2′-[(S)-thio­phene-2,5-diylbis(carbonyl­aza­nedi­yl)]dipropano­ate

The asymmetric unit of the title compound, C26H26N2O6S, contains two independent mol­ecules; each has twofold symmetry with the S atom and the mid-point of the C—C bond of the thio­phene ring located on a twofold rotation axis. In the two mol­ecules, the terminal benzene rings are oriented at dihedral angles of 65.8 (3) and 63.5 (3)° with respect to the central thio­phene rings. The meth­oxy­carbonyl group of one mol­ecule is disordered over two positions with site-occupancy factors of 0.277 (12) and 0.723 (12). Inter­molecular N—H⋯O hydrogen bonding is present in the crystal structure

Prediction models for solitary pulmonary nodules based on curvelet textural features and clinical parameters

Lung cancer, one of the leading causes of cancer-related deaths, usually appears as solitary pulmonary nodules (SPNs) which are hard to diagnose using the naked eye. In this paper, curvelet-based textural features and clinical parameters are used with three prediction models [a multilevel model, a least absolute shrinkage and selection operator (LASSO) regression method, and a support vector machine (SVM)] to improve the diagnosis of benign and malignant SPNs. Dimensionality reduction of the original curvelet-based textural features was achieved using principal component analysis. In addition, non-conditional logistical regression was used to find clinical predictors among demographic parameters and morphological features. The results showed that, combined with 11 clinical predictors, the accuracy rates using 12 principal components were higher than those using the original curvelet-based textural features. To evaluate the models, 10-fold cross validation and back substitution were applied. The results obtained, respectively, were 0.8549 and 0.9221 for the LASSO method, 0.9443 and 0.9831 for SVM, and 0.8722 and 0.9722 for the multilevel model. All in all, it was found that using curvelet-based textural features after dimensionality reduction and using clinical predictors, the highest accuracy rate was achieved with SVM. The method may be used as an auxiliary tool to differentiate between benign and malignant SPNs in CT images

Autism Risk Gene Cul3 Alters Neuronal Morphology via Caspase-3 Activity in Mouse Hippocampal Neurons

Autism Spectrum Disorders (ASDs) are neurodevelopmental disorders (NDDs) in which children display differences in social interaction/communication and repetitive stereotyped behaviors along with variable associated features. Cul3, a gene linked to ASD, encodes CUL3 (CULLIN-3), a protein that serves as a key component of a ubiquitin ligase complex with unclear function in neurons. Cul3 homozygous deletion in mice is embryonic lethal; thus, we examine the role of Cul3 deletion in early synapse development and neuronal morphology in hippocampal primary neuronal cultures. Homozygous deletion of Cul3 significantly decreased dendritic complexity and dendritic length, as well as axon formation. Synaptic spine density significantly increased, mainly in thin and stubby spines along with decreased average spine volume in Cul3 knockouts. Both heterozygous and homozygous knockout of Cul3 caused significant reductions in the density and colocalization of gephyrin/vGAT puncta, providing evidence of decreased inhibitory synapse number, while excitatory synaptic puncta vGulT1/PSD95 density remained unchanged. Based on previous studies implicating elevated caspase-3 after Cul3 deletion, we demonstrated increased caspase-3 in our neuronal cultures and decreased neuronal cell viability. We then examined the efficacy of the caspase-3 inhibitor Z-DEVD-FMK to rescue the decrease in neuronal cell viability, demonstrating reversal of the cell viability phenotype with caspase-3 inhibition. Studies have also implicated caspase-3 in neuronal morphological changes. We found that caspase-3 inhibition largely reversed the dendrite, axon, and spine morphological changes along with the inhibitory synaptic puncta changes. Overall, these data provide additional evidence that Cul3 regulates the formation or maintenance of cell morphology, GABAergic synaptic puncta, and neuronal viability in developing hippocampal neurons in culture