10948042
High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements
Approximately 80 long interspersed element (LINE-1 or L1) copies are able to retrotranspose actively in the human genome, and these are termed retrotransposition-competent L1s. The 5′ untranslated region (UTR) of the human-specific L1 contains an internal promoter and several transcription factor binding sites. To better understand the effect of the L1 5′ UTR on the evolution of human-specific L1s, we examined this population of elements, focusing on the sequence diversity and accumulated substitutions within their 5′ UTRs. Using network analysis, we estimated the age of each L1 component (the 5′ UTR, ORF1, ORF2, and 3′ UTR). Through the comparison of the L1 components based on their estimated ages, we found that the 5′ UTR of human-specific L1s accumulates mutations at a faster rate than the other components. To further investigate the L1 5′ UTR, we examined the substitution frequency per nucleotide position among them. The results showed that the L1 5′ UTRs shared relatively conserved transcription factor binding sites, despite their high sequence diversity. Thus, we suggest that the high level of sequence diversity in the 5′ UTRs could be one of the factors controlling the number of retrotransposition-competent L1s in the human genome during the evolutionary battle between L1s and their host genomes.
15872751
Human Genomic Deletions Generated by SVA-Associated Events
Mobile elements are responsible for half of the human genome. Among the elements, L1 and Alu are most ubiquitous. They use L1 enzymatic machinery to move in their host genomes. A significant amount of research has been conducted about these two elements. The results showed that these two elements have played important roles in generating genomic variations between human and chimpanzee lineages and even within a species, through various mechanisms. SVA elements are a third type of mobile element which uses the L1 enzymatic machinery to propagate in the human genome but has not been studied much relative to the other elements. Here, we attempt the first identification of the human genomic deletions caused by SVA elements, through the comparison of human and chimpanzee genome sequences. We identified 13 SVA recombination-associated deletions (SRADs) and 13 SVA insertion-mediated deletions (SIMDs) in the human genome and characterized them, focusing on deletion size and the mechanisms causing the events. The results showed that the SRADs and SIMDs have deleted 15,752 and 30,785 bp, respectively, in the human genome since the divergence of human and chimpanzee and that SRADs were caused by two different mechanisms, nonhomologous end joining and nonallelic homologous recombination.
23879241
Less is more: management of pediatric splenic injury.
OBJECTIVE
To analyze national trends in the nonoperative management of pediatric splenic injury.


DESIGN
Retrospective cohort analysis.


PATIENTS
All children and adolescents 18 years or younger from 2 national databases who were hospitalized with pediatric splenic injury.


SETTING
Data from 9 years of the National Inpatient Sample database (2000-2008) and 3 years of Kids' Inpatient Database (2000, 2003, and 2006).


MAIN OUTCOME MEASURES
We calculated and chronicled rates of splenectomy, angiography, and transfusion from 2000 to 2008.


RESULTS
During the study period, the rate of splenectomy decreased from 18.25% to 10.86%. Changes in nonoperative management included more than a 2-fold increase in angiography, from 2.43% to 6.94%, and a significant increase in transfusion, from 7.71% to 11.49%. Operative management was associated with increased length of stay (9.15 vs 6.52 days) and higher mean total hospital charges ($74 981.26 vs $36 156.30). Cases occurring in rural locations were more likely to undergo operative management (odds ratio, 1.24 [95% CI, 1.18-1.31]; P < .001), but less likely to undergo angiography (0.82 [0.76-0.89]; P < .001).


CONCLUSIONS
Children with pediatric splenic injury are undergoing fewer splenectomies but more angiography. Rural location may be an independent risk factor for operative management. Further studies are needed to assess for disparity in access to and availability of aggressive nonoperative management.
2718647
Bi-compartmental communication contributes to the opposite proliferative behavior of Notch1-deficient hair follicle and epidermal keratinocytes
Notch1-deficient epidermal keratinocytes become progressively hyperplastic and eventually produce tumors. By contrast, Notch1-deficient hair matrix keratinocytes have lower mitotic rates, resulting in smaller follicles with fewer cells. In addition, the ratio of melanocytes to keratinocytes is greatly reduced in hair follicles. Investigation into the underlying mechanism for these phenotypes revealed significant changes in the Kit, Tgfβ and insulin-like growth factor (IGF) signaling pathways, which have not been previously shown to be downstream of Notch signaling. The level of Kitl (Scf) mRNA produced by Notch1-deficient follicular keratinocytes was reduced when compared with wild type, resulting in a decline in melanocyte population. Tgfβ ligands were elevated in Notch1-deficient keratinocytes, which correlated with elevated expression of several targets, including the diffusible IGF antagonist Igfbp3 in the dermal papilla. Diffusible stromal targets remained elevated in the absence of epithelial Tgfβ receptors, consistent with paracrine Tgfβ signaling. Overexpression of Igf1 in the keratinocyte reversed the phenotype, as expected if Notch1 loss altered the IGF/insulin-like growth factor binding protein (IGFBP) balance. Conversely, epidermal keratinocytes contained less stromal Igfbp4 and might thus be primed to experience an increase in IGF signaling as animals age. These results suggest that Notch1 participates in a bi-compartmental signaling network that controls homeostasis, follicular proliferation rates and melanocyte population within the skin.
1814033
Mistaken Identity: Clarification of Rubus coreanus Miquel (Bokbunja)
In the U.S., there has been a recent surge in Korean black raspberry products available and in the number of reports about this species appearing in the scientific literature. Despite this, the majority of products sold and the work carried out has been on Rubus occidentalis L., not R. coreanus Miquel. The importance of accurate recognition of all starting material is multiplied for research downstream, including genetics/genomics, plant breeding, phenolic identification, food processing improvements and pharmacokinetic investigations. An overview of distinguishing characteristics separating R. coreanus from R. occidentalis will be presented. Research conducted on correctly identified fruit will also be summarized to aid future studies that might showcase the unique qualities that bokbunja can offer.
24325594
Population structure of and mycotoxin production by Fusarium graminearum from maize in South Korea.
Fusarium graminearum (Gibberella zeae) is an important pathogen of wheat, maize, barley, and rice in South Korea, and harvested grain often is contaminated with trichothecenes such as deoxynivalenol and nivalenol. In this study, we examined 568 isolates of F. graminearum collected from maize at eight locations in South Korea. We used amplified fragment length polymorphisms (AFLPs) to identify four lineages (2, 3, 6, and 7); lineage 7 was the most common (75%), followed by lineage 6 (12%), lineage 3 (12%), and lineage 2 (1%). The genetic identity among populations was high (>0.98), and the effective migration rate between locations was higher than that between lineages. Female fertility varied by lineage: all lineage 7 isolates were fertile, while 70%, 26%, and 14% of the isolates in lineages 6, 3, and 2, respectively, were fertile. All lineage 3 and lineage 7 isolates produced deoxynivalenol, whereas most lineage 2 and 6 isolates produced nivalenol. Genotypic diversity in lineage 3 and lineage 6 populations is similar to that found in previously described Korean rice populations, but genotypic diversity in lineage 7 is much lower, even though similar levels of gene flow occur between lineage 7 populations. We conclude that lineage 7 was relatively recently introduced into South Korea, perhaps accompanying imported maize seeds.
18820179
Marketplace Analysis Demonstrates Quality Control Standards Needed for Black Raspberry Dietary Supplements
There is currently no standard for the minimum anthocyanin concentration a black raspberry dietary supplement must contain for legal sale in the US. All consumer available black raspberry products (n = 19), packaged as dietary supplements or otherwise prepared (freeze-dried whole and pre-ground powders), were purchased and analyzed for their anthocyanin composition and concentration. Seven of the 19 samples contained no anthocyanins from black raspberry fruit, while three of those seven (without black raspberry fruit) had no anthocyanins of any kind. There was a wide range of anthocyanin concentration within the remaining products (18.1–2,904.8 mg/100 g; n = 12). When expressed as per capsule or per ∼1 teaspoon, concentration ranged from 0.1 to 145.2 mg (average 28 mg; n = 12). Until US dietary supplement labeling comes under regulatory oversight similar to food guidelines, foods are a more dependable source for dietary phenolics than supplements.