Evolution of MHC-G in humans and primates based on three new 3'UT polymorphisms

MHC-G is a class Ib (non-classical) major histocompatibility complex (MHC) whose functional and evolutionary characteristics are still under scrutiny. The study of noncoding sequences in the MHC genes may provide important phylogenetic information. In this work we have sequenced the MHC-G exon 8, which encodes for the 3'UT region, in different species of primates. It has been shown that: (1) a previously described 14 base pair (bp) deletion polymorphism is human-specific and the HLA-G alleles may be classified according to its absence or presence; (2) another newly described 3 bp deletion/insertion polymorphism is also human-specific; and (3) another newly described 51 bp deletion polymorphism is common to Pongidae and humans, but is not found in other primates belonging to the Cercopithecinae family. A hypothesis on the evolutionary pathway of this gene is put forward in the light of these findings.     

Shashi XLMR syndrome: report of a second family

This report describes a family with mental retardation in two brothers. The pedigree is consistent with either X-linked mental retardation or autosomal recessive inheritance. The clinical features consist of coarse face, prominent lower lip, large testes, and obesity. This same constellation of findings was observed in a family with X-linked mental retardation (XLMR) reported by Shashi et al. [2000: Am J Hum Genet 66:469-479]. Furthermore, haplotype analysis was consistent with localization of the Shashi XLMR syndrome in Xq26-q27. Thus, the family likely represents a second occurrence of the Shashi XLMR syndrome.     

Correcting signal biases and detecting regulatory elements in STARR-seq data

High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human genome at once. The resulting data, however, present substantial analytical challenges. Here, we identify technical biases that explain most of the variance in STARR-seq data. We then develop a statistical model to correct those biases and to improve detection of regulatory elements. This approach substantially improves precision and recall over current methods, improves detection of both activating and repressive regulatory elements, and controls for false discoveries despite strong local correlations in signal.

Gene regulation is of foundational importance to nearly all biological processes, and variation in gene regulatory activity plays a major role in human disease risk (Lee and Young 2013; Parker et al. 2013; Finucane et al. 2015). A major step toward measuring regulatory activity across the human genome has been the development of high-throughput reporter assays such as STARR-seq (Arnold et al. 2013) that allow regulatory element activity to be quantified with high-throughput sequencing rather than with optical detection of a fluorescent or luminescent signal.High-throughput reporter assays create substantial analytical challenges that are distinct from other sequencing-based genomic assays. There is significant local variation in high-throughput reporter assay signal. We show here that, across data from several laboratories, most of that variation can be explained by features of the underlying genomic sequence and experimental procedures rather than by regulatory element activity. For example, nucleotide composition can alter PCR efficiency leading to under- and overrepresentation of some sequences. Meanwhile, highly repetitive sequences often do not align uniquely to the human reference genome, also biasing signal estimates. Additional analytical challenges include that STARR-seq signals can be both positive and negative, reflecting activation and repression, and the boundaries of regulatory elements are typically unknown and must therefore be estimated from the data. Those challenges together impact signal representations, hinder estimation of regulatory element activity, and cause false positives and false negatives when left unaddressed.Taken together, key requirements of statistical methods to analyze STARR-seq data are the ability to identify and estimate the effect of both activating and repressing regulatory elements while also correcting for underlying sequence biases in high-throughput reporter assays. A statistical model was recently introduced that corrects technical biases and detects regulatory elements in STARR-seq, but the model is limited to detecting only activating regulatory elements (Lee et al. 2020). Considering repression is a crucial gene regulation mechanism (Courey and Jia 2001), overlooking repressive elements may limit understanding of gene regulation with STARR-seq. To overcome that challenge, our correcting reads and analysis of differentially active elements (CRADLE) model takes a two-step approach. First, CRADLE uses a generalized linear regression model to estimate and correct major biases that we have identified in STARR-seq data. Next, CRADLE detects regions with statistically significant regulatory activity from the bias-corrected signals while rigorously controlling FDR. In doing so, CRADLE substantially improves the use of STARR-seq by providing a robust estimation of regulatory activity and improved visualization of raw signals.     

Limb preference after unilateral pyramidotomy in adult and neonatal rats

As previously reported, unilateral pyramidotomy in newborn rats results in the development of an aberrant ipsilateral corticospinal tract that originates from the intact side. In the present study, limb preference after unilateral pyramidotomy in adult and neonatal rats was examined in search of differences that might correlate with this aberrant tract. However, no significant differences were observed between the two groups. Postoperatively, adult animals preferred the limb corresponding to the intact corticospinal tract in spite of a pre- and postoperative testing bias toward the opposite limb. Similarly, the animals that sustained neonatal lesion followed by testing at maturity also preferred the limb corresponding to the normal crossed corticospinal tract.     

Iron metabolism and fungal infections in patients with haematological malignancies.

AIM--To determine whether iron metabolism influences the incidence of systemic fungal infection in patients with haematological malignancies. METHODS--The study population comprised 74 patients who had undergone myeloablative chemotherapy. Systemic fungal infections were classified as confirmed (histological confirmation or characteristic septate hyphae) or possible (antibiotic resistant fever which resolved following administration of intravenous amphotericin B, together with either typical radiographic lesions or massive oropharyngeal candidiasis). Parameters of iron metabolism included serum iron concentrations, total iron binding capacity, serum transferrin, and ferritin concentrations and transferrin saturation values. RESULTS--Patients who developed a fungal infection had substantially increased transferrin saturation values and ferritin concentrations at diagnosis together with low serum transferrin and high serum iron concentrations. This profile was present in patients with a fungal infection regardless of the underlying haematological disorder. CONCLUSION--Increased transferrin saturation values and high ferritin concentrations may be additional risk factors for the development of systemic fungal infection in patients with haematological malignancies.     

Comparison of two copper IUDs: the MLCu375 and the Nova-T

A comparative randomized trial was carried out on two intrauterine contraceptive devices: the Nova-T and the MLCu375. The IUDs were used by 1116 and 1237 women respectively, over a period of 2 years. The reasons for IUD removal were analyzed after one and two years using the life-table method. Statistically significant differences were found in the rates for pregnancy, expulsion and removal for bleeding and/or pain favoring the MLCu375 IUD.

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Resumen Se hizo una prueba comparativa al azar de dos dispositivos anticonceptivos intrauterinos: el Nova-T y el MLCu375. Los DIU fueron usados por 1116 y 1237 mujeres respectivamente, durante un período de 2 años. Las razones para quitar un DIU fueron analizadas después de uno y dos años de uso empleando el método de tabla de vida. Se encontraron diferencias estadísticas significativas en las tasas de embarazo, expulsión y remoción por sangrado y/o dolor, siendo favorables para el MLCu375.

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Resumé Une étude comparative randomisée a été effectuée sur deux dispositifs contraceptifs intrautérins: le Nova-T et le MLCu375. Ces stérilets ont été utilisés respectivement par 1116 et 1237 femmes sur une période de deux ans. On a analysé après un an et après duex ans, par la méthode des tables de survie, les raisons pour lesquelles ces DIU avaient été abandonnés. Des différences significatives du point de vue statistique ont été constatées dans les taux de grossesse, d'expulsion et de retrait pour cause de saignement et/ou de douleurs, et ces différences étaient favorables au dispositif MLCu375.

     

Comparative performance of two copper IUDs: Nova-T and MLCu375

A comparative randomized trial was made of two intrauterine contraceptive devices: Nova-T and MLCu375. The IUDs were used by 637 and 606 women, respectively, for one year, unless the device was removed earlier. The reasons for IUD removal were analyzed after one year using the life-table method. Statistically significant differences were found in expulsion and removal for bleeding and/or pain rates.

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Sumario Se hizo un estudio comparativo al azar de dos dispositivos anticonceptivos intrauterinos: el NOVA T y el MLCu375. Durante un año, a menos que el dispositivo hubiese sido quitado antes, los DIU fueron usados por 637 y 606 mujeres respectivamente. Las razones de la remoción de un DIU fueron analizadas después de un año usando el método de la tabla de vida. Se encontraron diferencias estadisticamente significativas en tasas de expulsión y de remoción por sangrado y/o dolor.

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Resumé Une étude comparative randomisée a été effectuée sur deux dispositifs intrautérins contraceptifs: NOVA T et ML CU 375. Les DIU devaient être utilisés respectivement par 637 et 606 femmes, pendant une année, exception faite des cas où le stérilet a dû être retiré plus tôt. Les motifs du retrait ont été analysés une année plus tard grâce à la méthode des tables de survie. Les statistiques ont montré des différences significatives des taux d'expulsion et de retrait pour saignements ou douleurs.

     

Body Composition Changes after a Weight Loss Intervention: A 3-Year Follow-Up Study

Studies comparing different types of exercise-based interventions have not shown a consistent effect of training on long-term weight maintenance. The aim of this study was to compare the effects of exercise modalities combined with diet intervention on body composition immediately after intervention and at 3 years’ follow-up in overweight and obese adults. Two-hundred thirty-nine people (107 men) participated in a 6-month diet and exercise-based intervention, split into four randomly assigned groups: strength group (S), endurance group (E), combined strength and endurance group (SE), and control group (C). The body composition measurements took place on the first week before the start of training and after 22 weeks of training. In addition, a third measurement took place 3 years after the intervention period. A significant interaction effect (group × time) (p = 0.017) was observed for the fat mass percentage. It significantly decreased by 5.48 ± 0.65%, 5.30 ± 0.65%, 7.04 ± 0.72%, and 4.86 ± 0.65% at post-intervention for S, E, SE, and C, respectively. Three years after the intervention, the fat mass percentage returned to values similar to the baseline, except for the combined strength and endurance group, where it remained lower than the value at pre-intervention (p < 0.05). However, no significant interaction was discovered for the rest of the studied outcomes, neither at post-intervention nor 3 years later. The combined strength and endurance group was the only group that achieved lower levels of fat mass (%) at both post-intervention and 3 years after intervention, in comparison with the other groups.     

Exploratory Efficacy of Calcium-Vitamin D Milk Fortification and Periodontal Therapy on Maternal Oral Health and Metabolic and Inflammatory Profile

In this 2 × 2 factorial, outcome-assessor blinded, feasibility randomised trial we explored the effect of a non-pharmaceutical multi-component intervention on periodontal health and metabolic and inflammatory profiles among pregnant women with periodontitis receiving prenatal care in a Brazilian public health centre. 69 pregnant women (gestational age ≤20 weeks, T0) were randomly allocated into four groups: (1) fortified sachet (vitamin D and calcium) and powdered milk plus periodontal therapy during pregnancy (early PT) (n = 17); (2) placebo sachet and powdered milk plus early PT (n = 15); (3) fortified sachet and powdered milk plus late PT (after delivery) (n = 19); (4) placebo sachet and powdered milk plus late PT (n = 18). Third trimester (T1) and 6–8 weeks postpartum (T2) exploratory outcomes included periodontal health (% sites with bleeding on probing (BOP)), glucose, insulin, C-Reactive Protein, serum calcium and vitamin D. The mean BOP was significantly reduced in the early PT groups, while BOP worsened in the late PT groups. No significant effect of fortification on BOP was observed. Changes in glucose levels and variation on birthweight did not differ among groups This feasibility trial provides preliminary evidence for estimating the minimum clinically important differences for selected maternal outcomes. A large-scale trial to evaluate the interventions’ clinical benefits and cost-effectiveness is warranted.     

25-Hydroxyvitamin D and Cardiorespiratory Fitness in Prepubertal Overweight and Obese Children

Childhood obesity has become a major global health problem. Vitamin D deficiency and poor cardiorespiratory fitness are highly prevalent in children with overweight or obesity, but little is known about their relationships. In this study, we aimed to analyze the relationship between serum 25-hydroxyvitamin D (25(OH)D) and cardiorespiratory fitness parameters in prepubertal obese and overweight children. A cross-sectional design with a sample of 57 prepubertal children, aged 9–11 years, with overweight or obesity was used. The fasting concentration of 25(OH)D was analyzed with a chemiluminescent microparticle immunoassay. Fat and lean body masses were determined by using DXA. Maximal oxygen uptake (VO_2max) was measured with the maximal treadmill test. A total of 68.4% of the sample had sufficient levels of 25(OH)D. As expected, their cardiorespiratory fitness was poor compared with that of normal-weight children, but 60% of the group exceeded the median obesity-specific reference values. No differences were found between the sexes for relative VO_2max or 25(OH)D levels. Moreover, no correlations were found between 25(OH)D and body composition or cardiorespiratory parameters for sex or vitamin D groups. Vitamin D status seems not to be directly related to body composition or cardiorespiratory fitness in prepubertal overweight or obese children.