Unexpected Accumulation of ncm\u3csup\u3e5\u3c/sup\u3eU and ncm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU in a \u3cem\u3etrm9\u3c/em\u3e Mutant Suggests an Additional Step in the Synthesis of mcm\u3csup\u3e5\u3c/sup\u3eU and mcm\u3csup\u3e5\u3c/sup\u3es\u3csup\u3e2\u3c/sup\u3eU

Background Transfer RNAs are synthesized as a primary transcript that is processed to produce a mature tRNA. As part of the maturation process, a subset of the nucleosides are modified. Modifications in the anticodon region often modulate the decoding ability of the tRNA. At position 34, the majority of yeast cytosolic tRNA species that have a uridine are modified to 5-carbamoylmethyluridine (ncm5U), 5-carbamoylmethyl-2′-O-methyluridine (ncm5Um), 5-methoxycarbonylmethyl-uridine (mcm5U) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The formation of mcm5 and ncm5 side chains involves a complex pathway, where the last step in formation of mcm5 is a methyl esterification of cm5 dependent on the Trm9 and Trm112 proteins. Methodology and Principal Findings Both Trm9 and Trm112 are required for the last step in formation of mcm5 side chains at wobble uridines. By co-expressing a histidine-tagged Trm9p together with a native Trm112p in E. coli, these two proteins purified as a complex. The presence of Trm112p dramatically improves the methyltransferase activity of Trm9p in vitro. Single tRNA species that normally contain mcm5U or mcm5s2U nucleosides were isolated from trm9Δ or trm112Δ mutants and the presence of modified nucleosides was analyzed by HPLC. In both mutants, mcm5U and mcm5s2U nucleosides are absent in tRNAs and the major intermediates accumulating were ncm5U and ncm5s2U, not the expected cm5U and cm5s2U. Conclusions Trm9p and Trm112p function together at the final step in formation of mcm5U in tRNA by using the intermediate cm5U as a substrate. In tRNA isolated from trm9Δ and trm112Δ strains, ncm5U and ncm5s2U nucleosides accumulate, questioning the order of nucleoside intermediate formation of the mcm5 side chain. We propose two alternative explanations for this observation. One is that the intermediate cm5U is generated from ncm5U by a yet unknown mechanism and the other is that cm5U is formed before ncm5U and mcm5U

Coherence and entanglement in Grover and Harrow-Hassidim-Lloyd algorithm

Coherence, discord and geometric measure of entanglement are important tools for measuring physical resources. We compute them at every steps of the Grover's algorithm. We summarize these resources's patterns of change. These resources are getting smaller at the step oracle and are getting bigger or invariant at the step diffuser. This result is similar to the entanglement's pattern of change in Grover's algorithm. Furthermore, we compute GM at every steps of the Harrow-Hassidim-Lloyd algorithm

1-(2-Hydr­oxy-4,5-dimeth­oxyphen­yl)propan-1-one

In the title compound, C11H14O4, isolated from the stems of Trigonostemon xyphophylloides, an intra­molecular O—H⋯O hydrogen bond helps to establish an essentially planar conformation for the mol­ecule (r.m.s. deviation = 0.044 Å)

2-Hydr­oxy-1-methoxyxanthen-9-one monohydrate

In the title compound, C14H10O4·H2O, isolated from the roots of Calophyllum membranaceum, the xanthene ring system is almost planar (r.m.s. deviation = 0.008 Å). In the crystal structure, inter­molecular O—H⋯O and O—H⋯(O,O) hydrogen bonds connect the mol­ecules

Repetitive transcranial magnetic stimulation for stroke rehabilitation: insights into the molecular and cellular mechanisms of neuroinflammation

Stroke is a leading cause of mortality and disability worldwide, with most survivors reporting dysfunctions of motor, sensation, deglutition, cognition, emotion, and speech, etc. Repetitive transcranial magnetic stimulation (rTMS), one of noninvasive brain stimulation (NIBS) techniques, is able to modulate neural excitability of brain regions and has been utilized in neurological and psychiatric diseases. Moreover, a large number of studies have shown that the rTMS presents positive effects on function recovery of stroke patients. In this review, we would like to summarized the clinical benefits of rTMS for stroke rehabilitation, including improvements of motor impairment, dysphagia, depression, cognitive function, and central post-stroke pain. In addition, this review will also discuss the molecular and cellular mechanisms underlying rTMS-mediated stroke rehabilitation, especially immune regulatory mechanisms, such as regulation of immune cells and inflammatory cytokines. Moreover, the neuroimaging technique as an important tool in rTMS-mediated stroke rehabilitation has been discussed, to better understanding the mechanisms underlying the effects of rTMS. Finally, the current challenges and future prospects of rTMS-mediated stroke rehabilitation are also elucidated with the intention to accelerate its widespread clinical application

Transcriptome Analysis Suggests the Roles of Long Intergenic Non-coding RNAs in the Growth Performance of Weaned Piglets

Long intergenic non-coding RNAs (lincRNAs) have been considered to play a key regulatory role in various biological processes. An increasing number of studies have utilized transcriptome analysis to obtain lincRNAs with functions related to cancer, but lincRNAs affecting growth rates in weaned piglets are rarely described. Although lincRNAs have been systematically identified in various mouse tissues and cell lines, studies of lincRNA in pigs remain rare. Therefore, identifying and characterizing novel lincRNAs affecting the growth performance of weaned piglets is of great importance. Here, we reconstructed 101,988 lincRNA transcripts and identified 1,078 lincRNAs in two groups of longissimus dorsi muscle (LDM) and subcutaneous fat (SF) based on published RNA-seq datasets. These lincRNAs exhibit typical characteristics, such as shorter lengths and lower expression relative to protein-encoding genes. Gene ontology analysis revealed that some lincRNAs could be involved in weaned piglet related processes, such as insulin resistance and the AMPK signaling pathway. We also compared the positional relationship between differentially expressed lincRNAs (DELs) and quantitative trait loci (QTL) and found that some of DELs may play an important role in piglet growth and development. Our work details part of the lincRNAs that may affect the growth performance of weaned piglets and promotes future studies of lincRNAs for molecular-assisted development in weaned piglets

1-(5-Hydroxy-7-methoxy-2,2-dimethyl-2H-chromen-6-yl)ethan-1-one

The title chromene, C14H16O4, was isolated from the stems of Polyalthia plagioneura Diels. The mol­ecular structure is stabilized by an intra­molecular O–H⋯O hydrogen bond, which generates an S(6) ring. In the crystal, the mol­ecules are linked by C—H⋯O inter­actions, generating [010] chains

Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs

An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat development. Here, we used published RNA-seq data from subcutaneous adipose tissue of Italian Large White pigs and identified 252 putative lincRNAs, wherein 34 were unannotated. These lincRNAs had relatively shorter length, lower number of exons, and lower expression level compared with protein-coding transcripts. Gene ontology and pathway analysis indicated that the adjacent genes of lincRNAs were involved in lipid metabolism. In addition, differentially expressed lincRNAs (DELs) between low and high backfat thickness pigs were identified. Through the detection of quantitative trait locus (QTL), DELs were mainly located in QTLs related to adipose development. Based on the expression correlation of DEL genes and their differentially expressed potential target genes, we constructed a co-expression network and a potential pathway of DEL’s effect on lipid metabolism. Our study identified and analyzed lincRNAs in subcutaneous adipose tissue, and results suggested that lincRNAs may be involved in the regulation of subcutaneous fat development. Our findings provided new insights into the biological function of porcine lincRNAs