Time‐Varying Latent Effect Model for Longitudinal Data with Informative Observation Times

Summary In analysis of longitudinal data, it is not uncommon that observation times of repeated measurements are subject‐specific and correlated with underlying longitudinal outcomes. Taking account of the dependence between observation times and longitudinal outcomes is critical under these situations to assure the validity of statistical inference. In this article, we propose a flexible joint model for longitudinal data analysis in the presence of informative observation times. In particular, the new procedure considers the shared random‐effect model and assumes a time‐varying coefficient for the latent variable, allowing a flexible way of modeling longitudinal outcomes while adjusting their association with observation times. Estimating equations are developed for parameter estimation. We show that the resulting estimators are consistent and asymptotically normal, with variance–covariance matrix that has a closed form and can be consistently estimated by the usual plug‐in method. One additional advantage of the procedure is that it provides a unified framework to test whether the effect of the latent variable is zero, constant, or time‐varying. Simulation studies show that the proposed approach is appropriate for practical use. An application to a bladder cancer data is also given to illustrate the methodology.     

Flavinylation and Assembly of Succinate Dehydrogenase Are Dependent on the C-terminal Tail of the Flavoprotein Subunit

The enzymatic function of succinate dehydrogenase (SDH) is dependent on covalent attachment of FAD on the ∼70-kDa flavoprotein subunit Sdh1. We show presently that flavinylation of the Sdh1 subunit of succinate dehydrogenase is dependent on a set of two spatially close C-terminal arginine residues that are distant from the FAD binding site. Mutation of Arg⁵⁸² in yeast Sdh1 precludes flavinylation as well as assembly of the tetrameric enzyme complex. Mutation of Arg⁶³⁸ compromises SDH function only when present in combination with a Cys⁶³⁰ substitution. Mutations of either Arg⁵⁸² or Arg⁶³⁸/Cys⁶³⁰ do not markedly destabilize the Sdh1 polypeptide; however, the steady-state level of Sdh5 is markedly attenuated in the Sdh1 mutant cells. With each mutant Sdh1, second-site Sdh1 suppressor mutations were recovered in Sdh1 permitting flavinylation, stabilization of Sdh5 and SDH tetramer assembly. SDH assembly appears to require FAD binding but not necessarily covalent FAD attachment. The Arg residues may be important not only for Sdh5 association but also in the recruitment and/or guidance of FAD and or succinate to the substrate site for the flavinylation reaction. The impaired assembly of SDH with the C-terminal Sdh1 mutants suggests that FAD binding is important to stabilize the Sdh1 conformation enabling association with Sdh2 and the membrane anchor subunits.     

A membrane-integrated fermentation reactor system: its effects in reducing the amount of sub-raw materials for D-lactic acid continuous fermentation by Sporolactobacillus laevolacticus

Continuous fermentation by retaining cells with a membrane-integrated fermentation reactor (MFR) system was found to reduce the amount of supplied sub-raw material. If the amount of sub-raw material can be reduced, continuous fermentation with the MFR system should become a more attractive process for industrialization, due to decreased material costs and loads during the refinement process. Our findings indicate that the production rate decreased when the amount of the sub-raw material was reduced in batch fermentation, but did not decrease during continuous fermentation with Sporolactobacillus laevolacticus. Moreover, continuous fermentation with a reduced amount of sub-raw material resulted in a productivity of 11.2 g/L/h over 800 h. In addition, the index of industrial process applicability used in the MFR system increased by 6.3-fold as compared with the conventional membrane-based fermentation reactor previously reported, suggesting a potential for the industrialization of this D-lactic acid continuous fermentation process.     

p21, an important mediator of quiescence during pituitary tumor formation, is dispensable for normal pituitary development during embryogenesis

A delicate balance between proliferation and differentiation must be maintained in the developing pituitary to ensure the formation of the appropriate number of hormone producing cells. In the adult, proliferation is actively restrained to prevent tumor formation. The cyclin dependent kinase inhibitors (CDKIs) of the CIP/KIP family, p21, p27 and p57, mediate cell cycle inhibition. Although p21 is induced in the pituitary upon loss of Notch signaling or initiation of tumor formation to halt cell cycle progression, its role in normal pituitary organogenesis has not been explored. In wildtype pituitaries, expression of p21 is limited to a subset of cells embryonically as well as during the postnatal proliferative phase. Mice lacking p21 do not have altered cell proliferation during early embryogenesis, but do show a slight delay in separation of proliferating progenitors from the oral ectoderm. By embryonic day 16.5, p21 mutants have an alteration in the spatial distribution of proliferating pituitary progenitors, however there is no overall change in proliferation. At postnatal day 21, there appears to be no change in proliferation, as assessed by cells expressing Ki67 protein. However, p21 mutant pituitaries have significantly less mRNA of Myc and the cyclins Ccnb1, Ccnd1, Ccnd2 and Ccne1 than wildtype pituitaries. Interestingly, unlike the redundant role in cell cycle inhibition uncovered in p27/p57 double mutants, the pituitary of p21/p27 double mutants has a similar proliferation profile to p27 single mutants at the time points examined. Taken together, these studies demonstrate that unlike p27 or p57, p21 does not play a major role in control of progenitor proliferation in the developing pituitary. However, p21 may be required to maintain normal levels of cell cycle components.     

Prevention of liver ischemia reperfusion injury by a combined thyroid hormone and fish oil protocol

Several preconditioning strategies are used to prevent ischemia–reperfusion (IR) liver injury, a deleterious condition associated with tissue resection, transplantation or trauma. Although thyroid hormone (T₃) administration exerts significant protection against liver IR injury in the rat, its clinical application is controversial due to possible adverse effects. Considering that prevention of liver IR injury has also been achieved by n-3 polyunsaturated fatty acid (n-3 PUFA) supplementation to rats, we studied the effect of n-3 PUFA dietary supplementation plus a lower dose of T₃ against IR injury. Male Sprague-Dawley rats receiving fish oil (300 mg/kg) for 3 days followed by a single intraperitoneal dose of 0.05 mg T₃/kg were subjected to 1 h of ischemia followed by 20 h of reperfusion. Parameters of liver injury (serum transaminases, histology) and oxidative stress (liver contents of GSH and oxidized proteins) were correlated with fatty acid composition, NF-κB activity, and tumor necrosis factor-α (TNF-α) and haptoglobin expression. IR significantly modified liver histology; enhanced serum transaminases, TNF-α response or liver oxidative stress; and decreased liver NF-κB activity and haptoglobin expression. Although IR injury was not prevented by either n-3 PUFA supplementation or T₃ administration, substantial decrease in liver injury and oxidative stress was achieved by the combined protocol, which also led to increased liver n-3 PUFA content and decreased n-6/n-3 PUFA ratios, with recovery of NF-κB activity and TNF-α and haptoglobin expression. Prevention of liver IR injury achieved by a combined protocol of T₃ and n-3 PUFA supplementation may represent a novel noninvasive preconditioning strategy with potential clinical application.     

The application of Au nanoclusters in the fluorescence imaging of human serum proteins after native PAGE: enhancing detection by low-temperature plasma treatment

Proteins in human serum are increasingly being studied for their roles in a wide variety of biochemical interactions. To improve the sensitivity of the detection of human serum proteins after native polyacrylamide gel electrophoresis (PAGE), we have developed a fluorescence imaging detection technique for the detection. BSA (bovine serum albumin)-stabilized Au nanoclusters (NCs) were applied as fluorescent probes for imaging, and low-temperature plasma (LTP) treatment of the Au NCs was introduced to enhance the fluorescence imaging. Here, a series of optimization experiments (e.g. those to optimize for pH) were conducted for protein detection after 1-DE and 2-DE, and several types of discharge gases (He, O(2), and N(2)) were selected for the LTP treatment. The possible mechanism of interaction between the proteins and the Au NCs was demonstrated by an isothermal titration calorimetry experiment. Using the present method, a sensitivity of 7-14 times higher than that of traditional staining detection methods was observed in the oxygen LTP-treated Au NCs fluorescence images, and some relatively low abundance proteins (identified by the MS/MS technique) were easily detected. In addition, this fluorescence imaging method was applied to distinguish between the serum samples of patients with liver diseases and those of healthy people. Thus, this fluorescence imaging method is suitable for the highly sensitive detection of various serum proteins, and it shows potential capabilities for clinical diagnosis.     

The N-glycans of Trichomonas vaginalis contain variable core and antennal modifications

Trichomonad species are widespread unicellular flagellated parasites of vertebrates which interact with their hosts through carbohydrate-lectin interactions. In the past, some data have been accumulated regarding their lipo(phospho)glycans, a major glycoconjugate on their cell surfaces; on the other hand, other than biosynthetic aspects, few details about their N-linked oligosaccharides are known. In this study, we present both mass spectrometric and high-performance liquid chromatography data about the N-glycans of different strains of Trichomonas vaginalis, a parasite of the human reproductive tract. The major structure in all strains examined is a truncated oligomannose form (Man(5)GlcNAc(2)) with α1,2-mannose residues, compatible with a previous bioinformatic examination of the glycogenomic potential of T. vaginalis. In addition, dependent on the strain, N-glycans modified by pentose residues, phosphate or phosphoethanolamine and terminal N-acetyllactosamine (Galβ1,4GlcNAc) units were found. The modification of N-glycans by N-acetyllactosamine in at least some strains is shared with the lipo(phospho)glycan and may represent a further interaction partner for host galectins, thereby playing a role in binding of the parasite to host epithelia. On the other hand, the variation in glycosylation between strains may be the result of genetic diversity within this species.     

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice (Oryza sativa), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or 24 nucleotides in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown. Here we examine the rice Dicer-Like (DCL) family, including OsDCL1, -3a, -3b and -4. By deep sequencing of small RNAs from different tissues of the wild type and osdcl4-1, we revealed that the processing of 21-nucleotide siRNAs, including trans-acting siRNAs (tasiRNA) and over 1000 phased small RNA loci, was largely dependent on OsDCL4. Surprisingly, the processing of 24-nucleotide phased small RNA requires the DCL3 homolog OsDCL3b rather than OsDCL3a, suggesting functional divergence within DCL3 family. RNA ligase-mediated 5' rapid amplification of cDNA ends and parallel analysis of RNA ends (PARE)/degradome analysis confirmed that most of the 21- and 24-nucleotide phased small RNA clusters were initiated from the target sites of miR2118 and miR2275, respectively. Furthermore, the accumulation of the two triggering miRNAs requires OsDCL1 activity. Finally, we show that phased small RNAs are preferentially produced in the male reproductive organs and are likely to be conserved in monocots. Our results revealed significant roles of OsDCL4, OsDCL3b and OsDCL1 in the 21- and 24-nucleotide phased small RNA biogenesis pathway in rice.     

Synthesis and biological evaluation of 7-O-modified oroxylin A derivatives

Oroxylin A (5,7-dihydroxy-6-methoxyflavone) is a naturally occurring monoflavonoid isolated from the root of Scutellaria baicalensis Georgi, and exhibits potent anticancer activities in vitro and in vivo. In this study, we synthesized three series of oroxylin derivatives by connecting a nitrogen-containing hydrophilic, heterocyclic ring to the C7-OH via a varying length of carbon chain. All the derivatives were screened for anti-proliferative activities against three tumor cell lines. Some of the derivatives displayed higher activities compared to oroxylin A. The most potent antitumor compound, 5f, also induced apoptosis in HepG2 cell. The difference of 5f between the inhibiting rates of cell proliferation and the apoptotic rates indicated that 5f was more likely to be a necrosis-inducing agent or both apoptosis/necrosis inducer.