Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons.
The long interspersed element-1 (LINE-1 or L1) is a highly successful retrotransposon in mammals. L1 elements have continued to actively propagate subsequent to the human-chimpanzee divergence, approximately 6 million years ago, resulting in species-specific inserts. Here, we report a detailed characterization of chimpanzee-specific L1 subfamily diversity and a comparison with their human-specific counterparts. Our results indicate that L1 elements have experienced different evolutionary fates in humans and chimpanzees within the past approximately 6 million years. Although the species-specific L1 copy numbers are on the same order in both species (1200-2000 copies), the number of retrotransposition-competent elements appears to be much higher in the human genome than in the chimpanzee genome. Also, while human L1 subfamilies belong to the same lineage, we identified two lineages of recently integrated L1 subfamilies in the chimpanzee genome. The two lineages seem to have coexisted for several million years, but only one shows evidence of expansion within the past three million years. These differential evolutionary paths may be the result of random variation, or the product of competition between L1 subfamily lineages. Our results suggest that the coexistence of several L1 subfamily lineages within a species may be resolved in a very short evolutionary period of time, perhaps in just a few million years. Therefore, the chimpanzee genome constitutes an excellent model in which to analyze the evolutionary dynamics of L1 retrotransposons.

title: Human Genomic Deletions Generated by SVA-Associated Events
abstract: 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.

title: High Levels of Sequence Diversity in the 5′ UTRs of Human-Specific L1 Elements
abstract: 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.

title: Genetic diversity and fitness of Fusarium graminearum populations from rice in Korea.
abstract: Fusarium graminearum is an important fungal pathogen of cereal crops and produces mycotoxins, such as the trichothecenes nivalenol and deoxynivalenol. This species may be subdivided into a series of genetic lineages or phylogenetic species. We identified strains of F. graminearum from the Republic of Korea to lineage, tested their ability to produce nivalenol and deoxynivalenol, and determined the genetic composition and structure of the populations from which they were recovered. Based on amplified fragment length polymorphism (AFLP), PCR genotyping, and chemical analyses of trichothecenes, all 249 isolates from southern provinces belonged to lineage 6, with 241 having the nivalenol genotype and 8 having the deoxynivalenol genotype. In the eastern Korea province, we recovered 84 lineage 6 isolates with the nivalenol genotype and 23 lineage 7 isolates with the deoxynivalenol genotype. Among 333 lineage 6 isolates, 36% of the AFLP bands were polymorphic, and there were 270 multilocus haplotypes. Genetic identity among populations was high (>0.972), and genotype diversity was low (30 to 58%). To test the adaptation of lineage 6 to rice, conidial mixtures of strains from lineages 3, 6, and 7 were inoculated onto rice plants and then recovered from the rice grains produced. Strains representing lineages 6 and 7 were recovered from inoculated spikelets at similar frequencies that were much higher than those for the strain representing lineage 3. Abundant perithecia were produced on rice straw, and 247 single-ascospore isolates were recovered from 247 perithecia. Perithecia representing lineage 6 (87%) were the most common, followed by those representing lineage 7 (13%), with perithecia representing lineage 3 not detected. These results suggest that F. graminearum lineage 6 may have a host preference for rice and that it may be more fit in a rice agroecosystem than are the other lineages present in Korea.

title: Development of near-infrared fluorophore (NIRF)-labeled activity-based probes for in vivo imaging of legumain.
abstract: Asparaginyl endopeptidase, or legumain, is a lysosomal cysteine protease that was originally identified in plants and later found to be involved in antigen presentation in higher eukaryotes. Legumain is also up-regulated in a number of human cancers, and recent studies suggest that it may play important functional roles in the process of tumorigenesis. However, detailed functional studies in relevant animal models of human disease have been hindered by the lack of suitably selective small molecule inhibitors and imaging reagents. Here we present the design, optimization, and in vivo application of fluorescently labeled activity-based probes (ABPs) for legumain. We demonstrate that optimized aza-peptidyl Asn epoxides are highly selective and potent inhibitors that can be readily converted into near-infrared fluorophore-labeled ABPs for whole body, noninvasive imaging applications. We show that these probes specifically label legumain in various normal tissues as well as in solid tumors when applied in vivo. Interestingly, addition of cell-penetrating peptides to the probes enhanced cellular uptake but resulted in increased cross-reactivity toward other lysosomal proteases as the result of their accumulation in lysosomes. Overall, we find that aza-peptidyl Asn ABPs are valuable new tools for the future study of legumain function in more complex models of human disease.

title: Effect of selenium fertilizer on free amino acid composition of broccoli (Brassica oleracea Cv. Majestic) determined by gas chromatography with flame ionization and mass selective detection.
abstract: Selenium-enriched broccoli florets, harvested from plants grown on soil fertilized with four levels of sodium selenate, were evaluated for their free amino acid composition using alkylchlorformate derivatization, solid-phase extraction, and GC-FID or GC-MS. The selenium-enriched florets contained 0.4 (control), 5.7 (treatment A), 98.6 (treatment B), and 879.2 (treatment C) microg/g Se (dry weight). Twenty-one free amino acids were identified in the control and all three treatments. The total free amino acid content of the broccoli florets ranged from 178 mmol/kg (dry weight), for the control, to 479 mmol/kg (dry weight), for treatment C. Broccoli from treatment C contained the highest level of Se, had the most total free amino acids, and had an extremely high level of glutamine (Gln) when compared to the control and the other two treatments. In general, the smallest addition of Se to the soil (treatment A) induced increased levels of all detectable amino acids when compared to the control, whereas increased additions of Se (treatments B and C) produced mixed responses. Florets from treatment A contained the highest essential amino acid content.

title: Marketplace Analysis Demonstrates Quality Control Standards Needed for Black Raspberry Dietary Supplements
abstract: 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.

title: Guns and states: pediatric firearm injury.
abstract: A recent report indicates that firearm-related injuries are responsible for 30% of pediatric trauma fatality. The literature is however limited in examining pediatric firearm injuries and variations in state gun control laws. Therefore, we sought to examine the association between pediatric firearm injuries and the Stand-Your-Ground (SYG) and Child Access Protection (CAP) laws.



All pediatric (age, 0-20 years) hospitalizations with firearm injuries were identified from the Kids' Inpatient Database from 2006 and 2009. States were compared for SYG and CAP laws.



A total of 19,233 firearm injury hospitalizations were identified, with 64.7% assault, 27.2% accidental, and 3.1% suicide injury. Demographics for assault injury were as follows: mean age of 17.6 years, 88.4% male, 44.4% black, 18.2% Hispanic, 70.5% from metropolitan areas, and 50.1% from the poorest median income neighborhoods. Suicide injury cases were more likely to be white (57.8% vs. 16.6%, p < 0.001) and female (15.1% vs. 9.8%, p < 0.001). States with the SYG law were associated with increased accidental injury (odds ratio [OR], 1.282; p < 0.001). There was no statistical association between CAP law and the incidence of accidental injury or suicide. Multivariate logistic regression analysis found other predictive demographic factors for firearm injury: black (OR, 6.164), urban areas (OR, 1.557), poorest median income neighborhoods (OR, 2.785), male (OR, 28.602), and 16 years or older (OR, 37.308). Total economic burden was estimated at more than $1 billion dollars, with a median length of stay of 3 days, 8.4% discharge to rehabilitation, and 6.2% in-hospital mortality.



Pediatric firearm injuries continue to be a significant source of morbidity, mortality, and economic burden. A significant increase in accidental firearm injuries in states with the SYG law may highlight inadvertent effects of the law. Race, sex, and median income are additional contributing factors. Advocacy and focused educational efforts for specific socioeconomic and racial groups may potentially reduce firearm injuries.



Prognostic study, level II.