Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Valorisation of Biowastes for the Production of Green Materials Using Chemical Methods

With crude oil reserves dwindling, the hunt for a sustainable alternative feedstock for fuels and materials for our society continues to expand. The biorefinery concept has enjoyed both a surge in popularity and also vocal opposition to the idea of diverting food-grade land and crops for this purpose. The idea of using the inevitable wastes arising from biomass processing, particularly farming and food production, is, therefore, gaining more attention as the feedstock for the biorefinery. For the three main components of biomass—carbohydrates, lipids, and proteins—there are long-established processes for using some of these by-products. However, the recent advances in chemical technologies are expanding both the feedstocks available for processing and the products that be obtained. Herein, this review presents some of the more recent developments in processing these molecules for green materials, as well as case studies that bring these technologies and materials together into final products for applied usage

Compliance in oxygen saturation targeting in preterm infants : a systematic review

UNLABELLED: During oxygen therapy in preterm infants, targeting oxygen saturation is important for avoiding hypoxaemia and hyperoxaemia, but this can be very difficult and challenging for neonatal nurses. We systematically reviewed the qualitative and quantitative studies investigating the compliance in targeting oxygen saturation in preterm infants and factors that influence this compliance. We searched PubMed, Embase, Web of Science, Cochrane, CINAHL and ScienceDirect from 2000 to January 2015. Sixteen studies were selected, which involved a total of 2935 nurses and 574 infants. The studies varied in methodology, and we have therefore used a narrative account to describe the data. The main finding is that there is a low compliance in oxygen targeting; the upper alarm limits are inappropriately set, and maintaining the saturation (SpO2) below the upper limit presented particular difficulties. Although there is little data available, the studies indicate that training, titration protocols and decreasing workload could improve awareness and compliance. Automated oxygen regulations have been shown to increase the time that SpO2 is within the target range. CONCLUSION: The compliance in targeting oxygen during oxygen therapy in preterm infants is low, especially in maintaining the SpO2 below the upper limit. WHAT IS KNOWN: • The use of oxygen in preterm infants is vital, but the optimal strategyremains controversial. • Targeting SpO2 during oxygen therapy in preterm infants has beenshown to reduce mortality and morbidity. WHAT IS NEW: • Review of the literature showed that the compliance in targeting SpO2and alarm settings is low. • Creating awareness of risks of oxygen therapy and benefits in targeting,decreasing nurse/patient ratio and automated oxygen therapy couldincrease compliance

Correlation and Interchangeability of Venous and Capillary Blood Gases in Non-Critically Ill Neonates

Background: Venous blood gas (VBG) is frequently used in the neonatal unit as alternative for capillary blood gas (CBG). However, studies reporting correlation are conflicting and data on interchangeability in neonates are lacking. Objective: We investigated the correlation and interchangeability of the components between VBG and CBG in infants admitted to the neonatal intensive care unit. Methods: In a prospective study in the neonatal unit in Leiden University Medical Center (Netherlands), simultaneously VBG and CBG were withdrawn in neonates when both venous puncture and intravenous access as blood gas monitoring was indicated. From each blood gas analysis, a Pearson correlation, intraclass correlation, and Bland-Altman analysis was performed. Clinically acceptable difference for each blood gas value was defined up-front by means of an absolute difference: pH ± 0.05; partial pressure of carbon dioxide (pCO2) (±0.67 kPa = 5 mmHg); partial pressure of oxygen (pO2) (±0.67 kPa = 5 mmHg); base excess ± 3 mmol/l; and bicarbonate (HCO3-) ± 3 mmol/l. Results: In 93 patients [median gestational age 31 (IQR 29-34) weeks], 193 paired samples of VBG and CBG were collected. The Pearson correlation between VBG and CBG was very strong for pH (r = 0.79; P < 0.001), BE (r = 0.90; P < 0.001) and bicarbonate (r = 0.87; P < 0.001); strong for pCO2 (r = 0.68; P < 0.001); and moderate for pO2 (r = 0.31; P < 0.001). The percentage of the interchangeability within our acceptable absolute difference for pH was 88%, pCO2 72%, pO2 55%, BE 90%, and bicarbonate 94%. Conclusion: VBG and CBG in neonates are well correlated and mostly interchangeable, except for pO2

Long-term neurodevelopmental outcome in children after antenatal intravenous immune globulin treatment in fetal and neonatal alloimmune thrombocytopenia

Background: Children with fetal and neonatal alloimmune thrombocytopenia face increased risk of intracranial hemorrhage potentially leading to developmental impairment. To prevent intracranial hemorrhage, pregnant women with alloantibodies against fetal platelets are often treated with intravenous immunoglobulin. Intravenous immunoglobulin seems effective in vastly reducing the risk of fetal or neonatal bleeding complications. However, information on long-term neurodevelopment of these children is lacking. Objective: This study aimed to evaluate long-term neurodevelopmental outcome in children with fetal and neonatal alloimmune thrombocytopenia who were treated with intravenous immunoglobulin antenatally. Study Design: An observational cohort study was performed, including children of mothers treated with intravenous immunoglobulin during pregnancy because a previous child was diagnosed with fetal and neonatal alloimmune thrombocytopenia. Children were invited for a follow-up assessment including standardized cognitive and neurologic tests. The parents were asked to complete a behavioral questionnaire and school performance reports. The primary outcome was severe neurodevelopmental impairment, defined as severe cognitive impairment (intelligence quotient <70), cerebral palsy with Gross Motor Function Classification System Level ≥3, bilateral blindness, and/or bilateral deafness (requiring amplification). The secondary outcome was mild to moderate neurodevelopmental impairment, defined as either mild to moderate cognitive impairment (intelligence quotient <85), cerebral palsy with Gross Motor Function Classification System Level ≤2, minor neurologic dysfunction, vision loss, and/or hearing loss. Results: Between 2003 and 2017, 51 children were live-born after antenatal intravenous immunoglobulin treatment. One family moved abroad and was therefore not eligible for inclusion. In total, 82% (41/50) of the eligible cases were included for neurodevelopmental assessment at a median age of 9 years and 8 months. Severe neurodevelopmental impairment was not detected. The incidence of mild to moderate neurodevelopmental impairment was 14% (6/41; 95% confidence interval, 6%–29%). The children's mean cognitive score, behavioral scores, and academic achievement were not different from those observed in the Dutch norm groups. Neuroimaging was performed in 90% (37/41) of cases. Severe intracranial hemorrhage was diagnosed in 2 cases (5%), one antenatally before the start of intravenous immunoglobulin and the other case 1 day after birth. Both cases had a normal neurodevelopmental outcome. Conclusion: The risk of neurodevelopmental impairment in children whose mothers were treated for fetal and neonatal alloimmune thrombocytopenia with antenatal intravenous immunoglobulin is comparable to that reported in the general population

Clinical and molecular characterization of an infant with a tandem duplication and deletion of 19p13

Copy number variations (CNVs) on the short arm of chromosome 19 are relatively rare. We present a patient with a tandem de novo 3.9Mb duplication of 19p13.12p13.2 and an adjacent 288kb deletion of 19p13.12. The CNVs were detected by genome wide SNP-array and confirmed by fluorescence in situ hybridization. Mate-pair sequencing revealed two breakpoint junctions leading to a germline tandem inverted duplication and an adjacent deletion. The patient had a major congenital heart defect and refractory edema leading to metabolic and endocrinological disturbances. Further complications occurred due to refractory chylothorax, severe inflammatory response syndrome, and repeating sepsis. After 2 months, the child died due to intractable respiratory failure. The phenotype of this patient was compared with reported patients with overlapping deletions or duplications. We conclude that the congenital heart defect, respiratory insufficiency, and abnormal neurologic examination are most likely due the contiguous gene deletion/duplication

Spatial epigenetic control of mono- and bistable gene expression

Bistability in signaling networks is frequently employed to promote stochastic switch-like transitions between cellular differentiation states. Differentiation can also be triggered by antagonism of activators and repressors mediated by epigenetic processes that constitute regulatory circuits anchored to the chromosome. Their regulatory logic has remained unclear. A reaction-diffusion model reveals that the same reaction mechanism can support both graded monostable and switch-like bistable gene expression, depending on whether recruited repressor proteins generate a single silencing gradient or two interacting gradients that flank a gene. Our experiments confirm that chromosomal recruitment of activator and repressor proteins permits a plastic form of control; the stability of gene expression is determined by the spatial distribution of silencing nucleation sites along the chromosome. The unveiled regulatory principles will help to understand the mechanisms of variegated gene expression, to design synthetic genetic networks that combine transcriptional regulatory motifs with chromatin-based epigenetic effects, and to control cellular differentiation