Evidence consistent with human L1 retrotransposition in maternal meiosis I

We have used a unique polymorphic 3' transduction to show that a human L1, or LINE-1 (long interspersed nucleotide element-1), retrotransposition event most likely occurred in the maternal primary oocyte during meiosis I. We characterized a truncated L1 retrotransposon with a 3' transduction that was inserted, in a Dutch male patient, into the X-linked gene CYBB, thereby causing chronic granulomatous disease. We used the unique flanking sequence to localize the precursor L1 locus, LRE3, to chromosome 2q24.1. In a cell culture assay, the retrotransposition frequency of LRE3 is greater than that for any other element that has been tested to date. The patient's mother had two LRE3 alleles that differed slightly in the 3'-flanking genomic DNA. The patient had a single LRE3 allele that was identical to one of the maternal alleles; however, the patient's insertion matched the maternal LRE3 allele that he did not inherit. Other data indicate that there is only a small chance that the father (unavailable for analysis) carries the precursor LRE3 allele. In addition, paternal origin of the insertion would have required that an LRE3 mRNA transcribed before meiosis II be carried separately from its precursor LRE3 allele in the fertilizing sperm. Since the mother carries a potential precursor allele and the insertion was on the patient's maternal X chromosome, it is highly likely that the insertion originated during maternal meiosis I.     

Wnt signaling is a key mediator of Cdx1 expression in vivo

In the mouse, Cdx1 is essential for normal anteroposterior vertebral patterning through regulation of a subset of Hox genes. Retinoic acid (RA) and certain Wnts have also been implicated in vertebral patterning, although the relationship between these signaling pathways and the regulation of mesodermal Hox gene expression is not fully understood. Prior work has shown that Cdx1 is a direct target of both Wnt and retinoid signaling pathways, and might therefore act to relay these signals to the Hox genes. Wnt and RA are believed to impact on Cdx1 through an atypical RA-response element (RARE) and Lef/Tcf-response elements (LRE), respectively, in the proximal promoter. To address the roles of these regulatory motifs and pathways, we derived mice mutated for the LRE or the LRE plus the RARE. In contrast to RARE-null mutants, which exhibit limited vertebral defects, LRE-null and LRE+RARE-null mutants exhibited vertebral malformations affecting the entire cervical region that closely phenocopied the malformations seen in Cdx1-null mutants. Mutation of the LRE also greatly reduced induction of Cdx1 by RA, demonstrating a requirement for Wnt signaling in the regulation of this gene by retinoids. LRE and LRE+RARE mutants also exhibited vertebral fusions, suggesting a defect in somitogenesis. As Wnt signaling is implicated in somitogenesis upstream of the Notch pathway, it is conceivable that Cdx1 might play a role in this process. However, none of the Notch pathway genes assessed was overtly affected.     

Law and Society in Seattle: Law-Related Education as Culturally Responsive Teaching

In this article, I provide a portrait (Sara Lawrence-Lightfoot and Jessica Hoffman Davis 1997) of a renowned law-related education (LRE) program, its teacher, and four of its student-participants. Following the portrait, I discuss theoretical explanations for the success of ethnic-minority students in this and other LRE programs. These explanations include the nature of law as a difficult subject, the many convergences between culturally responsive teaching and LRE, and the relation of the content and methods of LRE to the cultural capital, interests, backgrounds, and ethnic identities of the students. I conclude with a discussion of the reciprocal nature of these processes, research on white teachers who are successful in multicultural contexts, the importance of challenging, accelerated classes, and an argument for expanding research on culturally responsive teaching and the achievement of students of color to include attention to the methods and materials of LRE.     

Periodical polydeoxynucleotides and DNA curvature

A theoretical method to predict DNA curvature was developed, and a strikingly good correlation between the experimental retardations and theoretical curvature of all the periodical biosynthetic DNAs so far reported in the literature was found. The analysis has been extended to G- and C-rich synthetic polynucleotides, which show a behavior in agreement with the theoretical prediction. A possible application of the method to biologically significant DNA tracts is shown in the case of the regulative region of one of the genes which code for the small subunit of ribulose-1,5-bisphosphate carboxylase in Pisum sativum. While curvature measurements have not so far been reported for this system, biochemical analysis has indicated short nucleotide sequences (boxes I-III) as recognition sites for regulative proteins. On the basis of the theoretical curvature profile of the region and of the electrophoretic retardation measurements of synthetic polynucleotides, obtained by ligating monomers mimicking the boxes, we suggest that the proteins could use DNA local curvature as structural motif in the recognition process.     

Clinical Benefit of Liver Stiffness Measurement at 3 Months after Kasai Hepatoportoenterostomy to Predict the Liver Related Events in Biliary Atresia

Background

The progression of hepatic fibrosis may result in decompensated hepatic failure with cirrhosis, liver related events (LRE) such as ascites, variceal bleeding, and death after successful and timely Kasai hepatoportoenterostomy (HPE) in biliary atresia. The aim of this study is to suggest clinical benefit of the liver stiffness measurement (LSM) using transient elastography at 3 months after the Kasai operation to predict LRE.

Methods

Between January 2007 and December 2011, 69 eligible biliary atresia patients who underwent Kasai HPE and performed transient elastography before and 3 months after HPE were included. The occurrences of LRE were analyzed for all patients. All patients were divided into 2 groups (with and without LRE) for comparison. Multivariate analysis was used to detect the independent risk factors of LRE. The area under the receiver operation characteristics curve (AUROC) was used to establish the LSM optimal cutoff value of 3 months after Kasai operation in predicting LRE.

Results

LSM value, aminotransferase, albumin, bilirubin, and PT-INR significantly differed among the two groups. Multivariate analysis demonstrated LSM value as the most powerful independent factor of the development of LRE. The cut-off value of 19.9 kPa was calculated to be optimal for predicting LRE development with total sensitivity and specificity of 1.804. AUROC resulted in 0.943, with sensitivity of 85.3% and specificity of 95.2%.

Conclusions

The LSM value of 3 months after Kasai HPE can be a useful predictor of LRE development.     

Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models.

A map of local curvature of the pBR322 DNA has been established by electron microscopy analysis of linearized plasmid molecules. To determine their polarity these molecules are one end labelled with an avidin-ferritin-biotin complex and the images are digitized. Local curvature is calculated from two mathematical treatments of the DNA trajectory and expressed in term of a mean dinucleotide wedge angle. Eight regions of curvature are distinguished. The four main regions of curvature have a high content of phased AA runs. The experimental curvature map is compared to theoretical maps of curvature obtained from four available models for DNA curvature.     

Lifetime reproductive effort in humans

Lifetime reproductive effort (LRE) measures the total amount of metabolized energy diverted to reproduction during the lifespan. LRE captures key components of the life history and is particularly useful for describing and comparing the life histories of different organisms. Given a simple energetic production constraint, LRE is predicted to be similar in value for very different life histories. However, humans have some unique ecological characteristics that may alter LRE, such as the long post-reproductive lifespan, lengthy juvenile period and the cooperative nature of human foraging and reproduction. We calculate LRE for natural fertility human populations, compare the findings to other mammals and discuss the implications for human life-history evolution. We find that human life-history traits combine to yield the theoretically predicted value (approx. 1.4). Thus, even with the subsidized energy budget and uniqueness of the adult lifespan, human reproductive strategies converge on the same optimal value of LRE. This suggests that the fundamental demographic variables contained in LRE trade-off against one another in a predictable and highly constrained manner.     

利用指骨弯曲程度推断化石人猿超科成员移动行为方式的新方法:以禄丰古猿为例

长久以来,指骨弯曲程度都被用来推断化石灵长类移动行为方式。此前已有一些方法被提出并用于定量化比较指骨弯曲程度,包括半径弯曲程度法（radius of curvature）、夹角法（included angle, IA）、标准化矩臂弯曲程度法（normalized curvature moment arm, NCMA）以及高精度多项式曲线拟合法（high-resolution polynomial curve fitting, HR-PCF）。然而,在对指骨弯曲程度进行定量化的过程中,这些方法都显示出了理论或技术上的局限性。因此,在运用这些方法之前,应当谨慎考虑其适用性和精确程度对分析结果所产生的影响。鉴于此,为了避免先前方法中存在的问题并更加精确地定量描述指骨弯曲程度,本文介绍了一种新方法作为替代。该方法基于对指骨侧视图背侧轮廓曲线几何形态测量学标志点数据的四阶多项式曲线拟合,称为几何形态测量学—多项式曲线拟合法（4th order polynomial curve fitting on geometric morphometric landmark data, GM-PCF）。它以标准化指骨曲线高度（normalized phalangeal curve height, NPCH）作为指骨弯曲程度的定量指标,并且可以将平均标准化指骨曲线进行可视化以用于其弯曲程度的直观对比。此外,它还可以提供在解释指骨弯曲程度的功能意义中非常关键的指骨（背侧轮廓曲线）长度比例信息。GM-PCF还能够分析化石中常见的不完整的指骨。为了检验新方法的适用性,我们从现生类人猿（anthropoids）中选取了15个涵盖灵长类大部分移动行为方式的类群作为参考样本,采用GM-PCF方法对其指骨弯曲程度进行了定量分析,结果表明标准化指骨曲线高度（NPCH）对灵长类移动行为方式有很好的指示意义,配合指骨曲线长度,还可以更进一步了解树栖四足行走（arboreal quadrupedalism）、悬垂（suspension）与摆荡（brachiation）等行为与灵长类体型大小的关系。作为个案,我们采用新方法对中国中新世的两种禄丰古猿（禄丰禄丰古猿Lufengpithecus lufengensis和蝴蝶禄丰古猿Lufengpithecus hudienensis）的指骨弯曲程度与参考样本进行了对比,并根据对比结果对其最为可能的移动行为方式偏好进行了推断。     

Full-Length L1 Elements Have Arisen Recently in the Same 1-kb Region of the Gorilla and Human Genomes

New copies of the mammalian retrotransposon L1 arise in the germline at an undetermined rate. Each new L1 copy appears at a specific evolutionary time point that can be estimated by phylogenetic analysis. In humans, the active L1 sequence L1.2 resides at the genomic locus LRE1. Here we analyzed the region surrounding the LRE1 locus in humans and gorillas to determine the evolutionary history of the region and to estimate the age of L1.2. We found that the region was composed of an ancient L1, L1Hs-Lrg, which was significantly divergent from all other L1 sequences available in the databases. We also determined that L1.2 was absent from the gorilla genome and arose in humans after the divergence of gorilla and human lineages. In the gorilla LRE1 region, we discovered a different full-length L1 element, L1Gg-1, which was allelic and present at a high gene frequency in gorillas but absent from other primates. We determined the nucleotide sequence of L1Gg-1 and found that it was 98% identical to L1.2, suggesting a close relationship between active L1s in gorillas and humans. Received: 28 December 1997 / Accepted: 20 March 1998     

Three-dimensional ultrastructure of anionic sites of the glomerular basement membrane by a quick-freezing and deep-etching method using a cationic tracer

The ultrastructure of anionic sites in the lamina rara externa (LRE) of rat glomerular basement membrane (GBM) was studied in three dimensions by a quick-freezing and deep-etching method using polyethyleneimine (PEI) as a cationic tracer. Results were compared with those obtained with conventional ultrathin sections examined by transmission electron microscopy. Examination with the quick-freezing and deep-etching method was done without (group 1) or with (group 2) contrasting/fixation with a phosphotungstic acid and glutaraldehyde mixture and post-fixation with osmium tetroxide, which were necessary for visualization of PEI particles by conventional ultrathin sections. Using the quick-freezing and deep-etching method without following contrasting/fixation and post-fixation (group 1), many PEI particles were observed to decorate around fibrils, which radiated perpendicularly from the lamina densa to connect with the podocyte cell membrane. The arrangement of PEI particles was not as regular as that previously reported using conventional ultrathin sections. In contrast, the tissue that was studied with quick-freezing and deep-etching followed by contrasting/fixation and post-fixation (group 2) showed a shrunken appearance. The arrangement of PEI particles was regular (about 20 particles/1000 nm of LRE) as that previously observed using conventional ultrathin sections. However, the number of PEI particles on the LRE was markedly decreased and interruption of decorated fibrils was prominent, as compared with group 1. Ultrastructural examination using conventional ultrathin sections with contrasting/fixation and post-fixation (group 3) demonstrated PEI particles on the LRE in reasonable amounts (18-21 particles/1000 nm of LRE) with fairly regular interspacing (45-65 nm) as reported previously.(ABSTRACT TRUNCATED AT 250 WORDS)