tRNA-derived fragments (tRFs) have been defined as a novel class of small noncoding RNAs. tRFs have been reported to be deregulated in cancer, but their biologic function remains to be fully understood. We have identified a new tRF (named tRFGlu, that is specifically expressed in healthy mammary glands but not in breast cancer (BC). Consistently, tRFtRFtRFtRF specifically interacts with nucleolin (NCL), an RNA-binding protein overexpressed in BC and able to repress the translation of p53 mRNA. The binding properties of NCL-tRFin silico and analyzed by EMSA assays, are congruent with a competitive displacement of p53 mRNA by tRFtRFGlu-derived fragment acts as a tumor-suppressor in breast cancer by targeting nucleolin.

Transfer RNA-derived small RNA (tsRNA)s are novel non-coding RNAs, expressed in a variety of tissues and organs. Two subtypes of tsRNAs have been reported: tRNA-derived stress-induced RNA (tiRNA)s and tRNA-derived fragment (tRF)s. tsRNAs have been reported to play essential roles and possess different biological functions in a variety of physiological activities. Recently, tsRNAs have been implicated in a large number of diseases, such as cancers (including breast cancer, ovarian cancer, lung cancer, prostate cancer, colorectal cancer, etc.), neurological disorders, viral infections, metabolic diseases and angiogenesis-related diseases. Although the biological functions of tsRNAs are still poorly understood, correlations between dysregulated tsRNA expression and disease development have been recently reported. Additionally, their capabilities as potential biomarkers for disease diagnosis and prognosis have been revealed in clinical studies. In this review, we summarize the current knowledge of tsRNAs, and discuss their potential clinical applications as biomarkers in different diseases. Although the regulation of tsRNAs is similar to miRNAs in regards to the related physiological and pathological processes, the higher stability and expression levels of tsRNAs place them as ideal biomarkers for the diagnosis and prognosis in cancer and other diseases. Therefore, it is worth to verify the possibility and reliability of these reported tsRNAs as potential biomarkers for clinical applications in disease diagnosis and prognosis.

Keywords: Transfer RNA-derived small RNA (tsRNA); biomarker; diagnosis.

Behavioral problems in young children can be assessed by asking their parents or teachers to rate their behaviors. Genetic analyses of parental ratings show relatively large heritabilities for emotional and behavioral problems in young children, but data from teachers for this age group are scarce. Sources of variation in the Teacher's Report Form (TRF) problem scales were examined. The TRF was completed for 211 Dutch 5-year-old twin pairs and 4 single twins. Twins rated by different teachers had higher means and variances than twins rated by the same teacher, in addition twin correlations were lower in this group. In both groups monozygotic (MZ) correlations were generally higher than dizygotic (DZ) correlations. A model for twin resemblance was tested that allowed for these effects. For 5 problem scales (Withdrawn, Social Problems, Aggressive Behavior, Rule Breaking Behavior and Attention Problems) a model with genetic and unique environmental sources of variation fitted best to the data. For 3 problem scales (Anxious/Depressed, Thought Problems and Somatic Complaints) there were familial influences but it was not possible to distinguish between common environmental influences or genetic influences. Heritability was 63% for Attention problems, around 45% for Withdrawn, Social Problems, Aggressive Behavior and Rule Breaking Behavior, and around 30% for Anxious/Depressed, Thought Problems and Somatic Complaints.

Time-resolved fluorescence spectroscopy (TRFS) is a powerful analytical tool for quantifying the biochemical composition of organic and inorganic materials. The potential of TRFS for tissue diagnosis has been recently demonstrated. To facilitate the translation of TRFS to the clinical arena, algorithms for online TRFS data analysis are essential. A fast model-free TRFS deconvolution algorithm based on the Laguerre expansion method has previously been introduced. One limitation of this method, however, is the need to heuristically select two parameters that are crucial for the accurate estimation of the fluorescence decay: the Laguerre parameter alpha and the expansion order. Here, a new implementation of the Laguerre deconvolution method is introduced, in which a nonlinear least-square optimization of the Laguerre parameter alpha is performed, and the optimal expansion order is selected based on a minimum description length criterion (MDL). In addition, estimation of the zero-time delay between the recorded instrument response and fluorescence decay is also performed based on normalized mean square error criterion (NMSE). The method is validated on experimental data from fluorescence lifetime standards, endogenous tissue fluorophores, and human tissue. The proposed automated Laguerre deconvolution method will facilitate online applications of TRFS, such as real-time clinical tissue diagnosis.

The RNA exosome is one of the main 3′ to 5′ exoribonucleases in eukaryotic cells. Although it is responsible for degradation or processing of a wide variety of substrate RNAs, it is very specific and distinguishes between substrate and non-substrate RNAs as well as between substrates that need to be 3′ processed and those that need to be completely degraded. This specificity does not appear to be determined by the exosome itself but rather by about a dozen other proteins. Four of these exosome cofactors have enzymatic activity, namely, the nuclear RNA-dependent ATPase Mtr4, its cytoplasmic paralog Ski2 and the nuclear non-canonical poly(A) polymerases, TrfTrfTrfTrfTrfTrf interaction disrupts specific TRAMP and exosome functions, including snoRNA processing.

Tandemly repetitive sequences are widespread in all eukaryotic genomes, but data on tandem repeats are limited in Zhikong scallop (Chlamys farreri). In the present study, paired-end sequencing of 2016 individual fosmid clones resulted in 3646 sequences. A total of 2,286,986 bp of genomic sequences were generated, representing approximately 1.84 per thousand of the Zhikong scallop genome. Using tandem repeats finder (TRF) software, a total of 2500 tandem repeats were found, including 313 satellites, 1816 minisatellites and 371 microsatellites. The cumulative length of tandem repeats was 552,558 bp, accounting for 24.16% of total length. Specifically, the length of microsatellites, minisatellites and satellites was 9425, 336,001 and 207,132 bp, accounting for 1.71, 60.81 and 37.49% of the length of tandem repeats, and 0.41, 14.69 and 9.06% of total length, respectively. The detailed information on the characteristic of all repeat units was also represented, which will provide a useful resource for physical mapping and better utilization of the existing genomic information in Zhikong scallop.

Antibodies raised in rabbits against a synthetic preparation of thyrotropin-releasing factor (TRF) were used in association with the immunoperoxidase histochemical technique to localize TRF in the rat median eminence. Using coronal sections cut through the mid-arcuate region, specific immuno-reactive material was observed in the medial and lateral regions of the superficial layer of the external median eminence.

In organisms of all three domains of life, a plethora of sRNAs (small regulatory RNAs) exists in addition to the well-known RNAs such as rRNAs, tRNAs and mRNAs. Although sRNAs have been well studied in eukaryotes and in bacteria, the sRNA population in archaea has just recently been identified and only in a few archaeal species. In the present paper, we summarize our current knowledge about sRNAs and their function in the halophilic archaeon Haloferax volcanii. Using two different experimental approaches, 111 intergenic and 38 antisense sRNAs were identified, as well as 42 tRFs (tRNA-derived fragments). Observation of differential expression under various conditions suggests that these sRNAs might be active as regulators in gene expression like their bacterial and eukaryotic counterparts. The severe phenotypes observed upon deletion and overexpression of sRNA genes revealed that sRNAs are involved in, and important for, a variety of biological functions in H. volcanii and possibly other archaea. Investigation of the Haloferax Lsm protein suggests that this protein is involved in the archaeal sRNA pathway.

BACKGROUND

The Tehuacán Valley is one of the areas of Mesoamerica with the oldest history of plant management. Homegardens are among the most ancient management systems that currently provide economic benefits to people and are reservoirs of native biodiversity. Previous studies estimated that 30% of the plant richness of homegardens of the region are native plant species from wild populations. We studied in Náhuatl communities the proportion of native plant species maintained in homegardens, hypothesizing to find a proportion similar to that estimated at regional level, mainly plant resources maintained for edible, medicinal and ornamental purposes.

METHODS

We analysed the composition of plant species of homegardens and their similarity with surrounding Cloud Forest (CF), Tropical Rainforest (TRF), Tropical Dry forest (TDF), and Thorn-Scrub Forest (TSF). We determined density, frequency and biomass of plant species composing homegardens and forests through vegetation sampling of a total of 30 homegardens and nine plots of forests, and documented ethnobotanical information on use, management, and economic benefits from plants maintained in homegardens.

RESULTS

A total of 281 plant species was recorded with 12 use categories, 115 ornamental, 92 edible, and 50 medicinal plant species. We recorded 49.8 ± 23.2 (average ± S.D.) woody plant species (shrubs and trees) per homegarden. In total, 34% species are native to the Tehuacán Valley and nearly 16% are components of the surrounding forests. A total of 176 species were cultivated through seeds, vegetative propagules or transplanted entire individual plants, 71 tolerated, and 23 enhanced. The highest species richness and diversity were recorded in homegardens from the CF zone (199 species), followed by those from the TRF (157) and those from the TDF (141) zones.

CONCLUSIONS

Homegardens provide a high diversity of resources for subsistence of local households and significantly contribute to conservation of native biodiversity. The highest diversity was recorded in homegardens where the neighbouring forests had the least diversity, suggesting that management of homegardens aims at compensating scarcity of naturally available plant resources. Cultivated species were markedly more abundant than plants under other management forms. Diversity harboured and management techniques make homegardens keystones in strategies for regional biodiversity conservation.

Though behavioral genetic studies of aggression have implicated heritable and environmental factors, there is limited understanding of how these factors influence aggression across different settings and over time. Ratings for 732 twins were collected from parents and teachers during middle childhood and early adolescence. Total aggression scores on the Child Behavioral Checklist (CBCL) and Teacher Report Form (TRF) were examined at each age, across both settings, and developmentally. In this sample, aggressive behavior was moderately to largely heritable at each age within the home (.76-.84) and school (.42-.61). Across each age, ratings by parents and teachers were moderately correlated (.19-.36). Genetic and environmental effects that were limited to a particular setting were important etiological factors for aggressive behavior consistently within each setting, while only genetic factors influenced levels of aggression across both settings. Stability during these ages was due to genetic effects common to each age and the persistence of child-specific environmental experiences within each setting. These results suggest that genetic and environmental influences on children's aggressive behavior are largely setting specific. Levels of aggression seen consistently across both settings are due to genetic influences. Developmentally stable levels of aggressive behavior result from genetic influences common to all ages and individual environmental influences whose effects persist across ages.

We assessed aging in continuous donor skin fibroblast cell line GGM5 up to the 25th passage by in vitro replicative senescence, telomere dynamics and chromosomal abnormalities. Cell proliferation rate increased from 0.84+/-0.26 (primary cells) to 1.20+/-0.17 (13-15 passage group) per day and reduced to 0.65+/-0.14 in 22-25 passages. Cell proliferation rate was reduced by 45.7% after 87.62 CPDs. Cell viability reduced from 100% to 97.4% up to the 25th passages. Frequency of beta gal(+) cells increased in successive passages and days in culture. The correlation coefficient between frequency of beta gal(+) cells and growth rate was -0.50 to -0.61. Loss of mean <em>TRF</em> length was 13.8 nucleotides (passage 15) to 95.4 nucleotides per cell division in later passages. All cells showed Robertsonian translocation in 22-25 passaged cells. The SCNT pre-implantation embryos production was highest (22.5%) in donor cells used from 10-15 passages as compared to early (<or=5) and late (22-25 passages). Our findings supports that cell proliferation rates, beta gal staining, mean <em>TRF</em> loss and karyological profile are useful marker for evaluation of competent nuclear donor.

This study describes a scanning time-resolved fluorescence spectroscopy (TRFS) system designed to continuously acquire fluorescence emission and to reconstruct fluorescence lifetime images (FLIM) from a luminal surface by using a catheter-based optical probe with rotary joint and pull-back device. The ability of the system to temporally and spectrally resolve the fluorescence emission from tissue was validated using standard dyes and tissue phantoms (e.g., ex vivo pig aorta phantom). Current results demonstrate that this system is capable to reliably resolve the fluorescence emission of multiple fluorophores located in the lumen; and suggest its potential for intravascular detection of distinct biochemical features of atherosclerotic plaques.

This study was carried out to examine associations between classroom climate and pupils' mental health in primary school, and whether pupils who had emotional and behavioural problems in the second grade are more vulnerable to the effects of a poor classroom climate 4 years later. The study was carried out by means of questionnaires to teachers. The students (n = 861) were surveyed in the second (aged 8 years, Time 1) and sixth grade (aged 12 years, Time 2). The Rutter Teacher Questionnaire (RB2) at Time 1 and the Teacher Report Form (TRF) at Time 2 were used to measure internalizing, externalizing and total problem scores. Classroom climate was measured using a composite variable at Time 2. The results show associations between poor sixth-grade classroom climate and an increase in emotional and behavioural problems in both boys and girls. In addition, the girls who were overall poorly adjusted, particularly those who had externalizing problems in the second grade, were especially vulnerable to a poor classroom climate in the sixth grade.

Urinary excretion of selected markers for renal injury, as well as urinary excretion rates of the thromboxane metabolite, 11-keto-thromboxane B2 (11k-TXB2), was studied in 36 male patients undergoing coronary bypass surgery using cardiopulmonary bypass (CPB). In all patients, excretion of both tubular (N-acetyl-beta-D-glucosaminidase [beta NAG]; alpha 1-microglobulin [alpha 1-MG]) and glomerular markers (albumin [Alb]; transferrin [Trf]; immunoglobulin G [IgG]) sharply increased on Day 1 after CPB, and they remained elevated throughout the observation period of 5 days. Urinary excretion rates of 11k-TXB2 markedly increased on Day 1 after surgery, and they rapidly decreased thereafter. In 12 of the 36 patients, a temporary increase of serum creatinine levels >> 1.30 mg/dl) was noted following surgery. A positive correlation was found between serum creatinine levels and excretion of the tubular enzyme beta NAG (r = 0.36; p < 0.05), but not between creatinine levels and alpha 1-MG or the glomerular markers. Furthermore, no correlation between urinary excretion of 11k-TXB2 and any of the urinary markers for renal injury could be detected. Our data do not strengthen the hypothesis that acute renal injury observed during CPB is related to exaggerated thromboxane biosynthesis in these patients. Monitoring of urinary markers for incipient renal damage, particularly excretion of beta NAG, might be of additional diagnostic value for detection of otherwise subclinical renal injury in patients undergoing CPB.

BACKGROUND

The availability of a suitable matrix reference material is essential for standardization of the immunoassays used to measure serum proteins. The earlier serum protein reference material ERM-DA470 (previously called CRM470), certified in 1993, has led to a high degree of harmonization of the measurement results. A new serum protein material has now been prepared and its suitability in term of homogeneity and stability has been verified; after characterization, the material has been certified as ERM-DA470k/IFCC.

METHODS

We characterized the candidate reference material for 14 proteins by applying a protocol that is considered to be a reference measurement procedure, by use of optimized immunoassays. ERM-DA470 was used as a calibrant.

RESULTS

For 12 proteins [α(2) macroglobulin (A2M), α(1) acid glycoprotein (orosomucoid, AAG), α(1) antitrypsin (α(1)-protease inhibitor, AAT), albumin (ALB), complement 3c (C3c), complement 4 (C4), haptoglobin (HPT), IgA, IgG, IgM, transferrin (TRF), and transthyretin (TTR)], the results allowed assignment of certified values in ERM-DA470k/IFCC. For CRP, we observed a bias between the lyophilized and liquid frozen materials, and for CER, the distribution of values was too broad. Therefore, these 2 proteins were not certified in the ERM-DA470k/IFCC. Different value transfer procedures were tested (open and closed procedures) and found to provide equivalent results.

CONCLUSIONS

A new serum protein reference material has been produced, and values have been successfully assigned for 12 proteins.

Loss of telomere repeat sequences occurs after each cell division and telomere shortening has been implicated in cellular senescence. The measurement of telomere length might therefore assess the lifespan of a cell. The aim of this study was to set up and validate a technique enabling the assessment of telomere length on tissue sections. Quantitative fluorescence in situ hybridization (Q-FISH) with telomeric probes was performed on smears and sections from cell preparations or human tissues. The mean fluorescence intensity of telomere spots (FI/spot) was automatically quantified by image analysis. Telomeric restriction fragment (TRF) length was assessed by Southern blotting. There was a positive significant correlation between telomere length, as assessed by Q-FISH, and TRF length determined by Southern blotting in corresponding samples (p < 0.01, r = 0.6 for tissue and p < 0.01, r = 0.79 for cells). FI/spot was higher on smears than on sections, but pairwise comparison showed a significant correlation both for cells and for tissues (r = 0.77, p < 0.001 for cells and p < or = 0.01, r = 0.64 for tissue). Finally, since telomere length is expected to shorten with age, FI/spot was assessed in liver samples according to the age of patients: a negative correlation was demonstrated (r = 0.76, p < 0.01). Inter-assay variation was 7% for Q-FISH performed on tissue sections and 12% on touch preparations. This study shows that Q-FISH can be performed with confidence on fixed frozen tissue sections in order to assess telomere length. It is an easy, accurate, and reproducible in situ method for assessing telomeres in the context of cell type and tissue architecture.

Over the last few decades there has been an increased concern about the health risks from exposure to metallic trace elements, including arsenic, because of their potential neurotoxic effects on the developing brain. This study assessed whether urinary arsenic (UA) levels are associated with attention performance and Attention-Deficit/Hyperactivity Disorder (ADHD) in children living in an area with high industrial and mining activities in Southwestern Spain. A cross-sectional study was conducted on 261 children aged 6-9 years. Arsenic levels were determined in urine samples. Attention was measured by using 4 independent tools: a) tests from the Behavioral Assessment and Research System (BARS) designed to measure attention function: Simple Reaction Time Test (RTT), Continuous Performance Test (CPT) and Selective Attention Test (SAT); b) AULA Test, a virtual reality (VR)-based test that evaluates children's response to several stimuli in an environment simulating a classroom; c) Child Behavior Checklist (CBCL), administered to parents; and d) Teacher's Report Form (TRF), administered to teachers. Multivariate linear and logistic regression models, adjusted for potential confounders, were used to estimate the magnitude of the association between UA levels and attention performance scores. Higher UA levels were associated with an increased latency of response in RTT (β = 12.3; 95% confidence interval (CI): 3.5-21.1) and SAT (β = 3.6; 95% CI: .4-6.8) as well as with worse performance on selective and focalized attention in the AULA test (β for impulsivity = .6; 95% CI: .1-1.1; β for inattention = .5; 95% CI: .03-1.0). A dose-response relationship was observed between UA levels and inattention and impulsivity scores. In contrast, results from the CBCL and TRF tests failed to show a significant association with UA levels. In conclusion, UA levels were associated with impaired attention/cognitive function, even at levels considered safe. These results provide additional evidence that postnatal arsenic exposure impairs neurological function in children.

All-trans retinoic acid (ATRA) is a potent inducer of cell differentiation and growth arrest. Here, we investigated ATRA-induced regulatory cascades associated with growth arrest of the human hepatoma cell line HepG2. ATRA induced >2-fold changes in the expression of 402 genes including 55 linked to cell-cycle regulation, cell growth or apoptosis during 48 h treatment. Computational search predicted that 250 transcriptional regulatory factors (TRFs) could recognize the proximal upstream regions of any of the 55 genes. Expression of 61 TRF genes was significantly changed during ATRA incubation, providing many potential regulatory edges. We focused on six TRFs that could regulate many of the 55 genes and found a total of 160 potential edges in which the expression of each of the genes was changed later than the expression change of the corresponding regulator. RNAi knockdown of the selected TRFs caused perturbation of the respective potential targets. The genes showed an opposite regulation pattern by ATRA and specific siRNA treatments were selected as strong candidates for direct TRF targets. Finally, 36 transcriptional regulatory edges were validated by chromatin immunoprecipitation. These analyses enabled us to depict a part of the transcriptional regulatory cascades closely linked to ATRA-induced cell growth arrest.

The effects of the time of day of drug administration on the subchronic toxicity and pharmacokinetics of gentamicin, as well as the role of feeding schedule on circadian rhythms, were investigated in mice. ICR male mice were housed in a light-dark (LD) cycle (12:12) with food and water ad libitum (ALF) or under a time-restricted feeding (TRF) schedule (feeding time: 8 h during the light phase) for 1 day or 14 days before drug administration. The animals were given a single subcutaneous dose of gentamicin 180 mg/kg for the kinetic studies and subcutaneous doses of gentamicin 180 mg/kg/day for 14 days or 220 mg/kg/day for 18 days for the subchronic toxicity studies. A significant dosing-time dependency was shown for mortality and body weight loss, with higher values at midlight and lower ones at the middark (p < 0.05). A significant circadian rhythm was also found for gentamicin kinetics in ALF mice, with the highest clearance at middark and the lowest one at midlight (p < 0.01). The kinetic rhythm of gentamicin coincided well with the toxicity rhythm of the drug. The TRF schedule had a marked influence on the rhythms of gentamicin kinetics and toxicity, showing lowest clearance and higher toxicity at middark. The rhythm of subchronic toxicity of gentamicin seems to be due, at least in part, to the rhythm in kinetics and is strongly influenced by the feeding schedule. Thus, the timing of dosing is an important factor in the kinetics and the subchronic toxicity of gentamicin administration in mice, and the manipulation of feeding schedule can modify the rhythm of the toxicity by changing the rhythm of gentamicin kinetics.

Emotional and behavioural problems and competencies in a nation-wide sample of referred selective mute children (SM) and matched non-referred controls, aged 4-16 years, were assessed by the Child Behaviour Checklist, (CBCL), Teacher Report Form (TRF) and Youth Self Report (YSR) (1). Main issues addressed were the co-variation of internalising and externalising problems reported across informants, whether there exists a pure externalising group of children with SM, and the nature of the internalising and externalising problems. The results show that the children with SM differed substantially from their peers in internalising problems as reported by the parents and the teachers. In contrast, the results on the YSR indicated an under-reporting of internalising problems. Externalising problems in SM were reported in a low to moderate degree by the parents only. No child with SM and pure externalising symptoms was found. The children with SM differed mostly from their peers on the withdrawn scale. On the item level, both the internalising and the externalising symptoms that best differentiated the children with SM from the controls support the notion of SM as an expression of social anxiety.

To determine if cartilage T1ρ and T2 relaxation time measures after ACL injury and prior to reconstruction (baseline) are associated with patient-reported outcomes at baseline, 6-months, and 1-year after surgery.

Fifty-four ACL-injured participants were scanned in both knees at baseline using 3T MR T1ρ and T2 mapping. Participants also completed Knee-injury and Osteoarthritis Outcome Score (KOOS) and Marx activity level questionnaires at baseline, 6-months, and 1-year after reconstruction. The difference between cartilage T1ρ or T2 of the injured and contralateral knee (side-to-side difference, SSD) was calculated to account for physiological variations among patients. Linear regression models were built to evaluate the association between the baseline SSD T1ρ or T2 and KOOS or Marx at all time points.

Higher baseline SSD T1ρ posterolateral tibia (pLT) was associated with worse KOOS in all subscales except symptoms at baseline, worse KOOS pain at 6-months, and worse KOOS in all subscales except sports function at 1-year. Higher baseline SSD T2 femoral trochlea (TrF) was associated with worse KOOS activities of daily living (ADL) at 1-year. Higher baseline SSD T1ρ pLT was associated with lower Marx activity level at 1-year. More severe cartilage lesions, as assessed by Whole-Organ MRI Scoring (WORMS), was significantly associated with worse KOOS pain at 6-months and 1-year.

T1ρ and T2 of cartilage after ACL injury were associated with KOOS after injury and both KOOS and Marx after reconstruction. Such associations may help clinicians stratify outcomes post-injury, and thus, improve patient management.