Diagnostic measures for severe acute malnutrition in Indian infants under 6 months of age: a secondary data analysis

Background Weight for length z-score (WLZ) < − 3 is currently used to define severe acute malnutrition (SAM) among infants. However, this approach has important limitations for infants younger than 6 months of age as WLZ cannot be calculated using WHO growth standards if infant length is < 45 cm. Moreover, length for age z-score (LAZ) and weight for length z-score (WLZ) are least reliable measures, with high chances of variation, and less chances of detecting undernutrition in under 6 months infants. The objective of the current analysis was to compare WLZ with WAZ and LAZ in a cohort of Indian infants in predicting the deaths between 6 weeks and 6 months of age. Methods The data was from an individually randomized trial conducted in slums of Delhi, India in which infants’ weight and length were measured at 6 weeks of age (at the time of the first immunization visit). Vital status of the infants was documented from 6 weeks to 6 months of age. The sensitivity, specificity, positive and negative predictive values, and positive and negative likelihood ratios were calculated for WAZ < -3, WLZ < -3, and LAZ < -3 for deaths between 6 weeks and 6 months of age. The receiver operating characteristics curve was calculated for each of the above anthropometric indicators. Results For deaths occurring between 6 weeks to 6 months of age, the specificity ranged between 85.9–95.9% for all three anthropometric indicators. However, the sensitivity was considerably higher for WAZ; it was 64.6% for WAZ < -3, 39.1% for LAZ < -3, and 25.0% for WLZ < -3. WAZ < -3 had higher area under curve (0.75; 95% CI: 0.68, 0.82) and hence, better discriminated deaths between 6 weeks and 6 months of age than WLZ < -3. The adjusted relative risk (RR 10.6, 95% CI 5.9, 18.9) and the population attributable fraction (PAF 57.9, 95% CI 38.8, 71.0%) of mortality was highest for WAZ < -3. Conclusions We found WAZ < -3 at 6 weeks of age to be a better predictor of death in the 6 weeks to 6 months of life in comparison to WLZ < -3 and LAZ < -3 and propose that it should be considered to diagnose SAM in this age group.publishedVersio

Shelterin components mediate genome reorganization in response to replication stress

The dynamic nature of genome organization impacts critical nuclear functions including the regulation of gene expression, replication, and DNA damage repair. Despite significant progress, the mechanisms responsible for reorganization of the genome in response to cellular stress, such as aberrant DNA replication, are poorly understood. Here, we show that fission yeast cells carrying a mutation in the DNA-binding protein Sap1 show defects in DNA replication progression and genome stability and display extensive changes in genome organization. Chromosomal regions such as subtelomeres that show defects in replication progression associate with the nuclear envelope in sap1 mutant cells. Moreover, high-resolution, genome-wide chromosome conformation capture (Hi-C) analysis revealed prominent contacts between telomeres and chromosomal arm regions containing replication origins proximal to binding sites for Taz1, a component of the Shelterin telomere protection complex. Strikingly, we find that Shelterin components are required for interactions between Taz1-associated chromosomal arm regions and telomeres. These analyses reveal an unexpected role for Shelterin components in genome reorganization in cells experiencing replication stress, with important implications for understanding the mechanisms governing replication and genome stability

Different SWI/SNF complexes coordinately promote R-loop- and RAD52-dependent transcription-coupled homologous recombination

The SWI/SNF family of ATP-dependent chromatin remodeling complexes is implicated in multiple DNA damage response mechanisms and frequently mutated in cancer. The BAF, PBAF and ncBAF complexes are three major types of SWI/SNF complexes that are functionally distinguished by their exclusive subunits. Accumulating evidence suggests that double-strand breaks (DSBs) in transcriptionally active DNA are preferentially repaired by a dedicated homologous recombination pathway. We show that different BAF, PBAF and ncBAF subunits promote homologous recombination and are rapidly recruited to DSBs in a transcription-dependent manner. The PBAF and ncBAF complexes promote RNA polymerase II eviction near DNA damage to rapidly initiate transcriptional silencing, while the BAF complex helps to maintain this transcriptional silencing. Furthermore, ARID1A-containing BAF complexes promote RNaseH1 and RAD52 recruitment to facilitate R-loop resolution and DNA repair. Our results highlight how multiple SWI/SNF complexes perform different functions to enable DNA repair in the context of actively transcribed genes.</p

Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability

Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3.</p

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

Eukaryotic genomes are folded into three-dimensional structures, such as self-associating topological domains, the borders of which are enriched in cohesin and CCCTC-binding factor (CTCF) required for long-range interactions1-7. How local chromatin interactions govern higher-order folding of chromatin fibers and the function of cohesin in this process remain poorly understood. Here we perform genome-wide chromatin conformation capture (Hi-C) analysis8 to explore the high-resolution organization of the Schizosaccharomyces pombe genome, which despite its small size exhibits fundamental features found in other eukaryotes9. Our analyses of wild type and mutant strains reveal key elements of chromosome architecture and genome organization. On chromosome arms, small regions of chromatin locally interact to form “globules”. This feature requires a function of cohesin distinct from its role in sister chromatid cohesion. Cohesin is enriched at globule boundaries and its loss causes disruption of local globule structures and global chromosome territories. By contrast, heterochromatin, which loads cohesin at specific sites including pericentromeric and subtelomeric domains9-11, is dispensable for globule formation but nevertheless affects genome organization. We show that heterochromatin mediates chromatin fiber compaction at centromeres and promotes prominent interarm interactions within centromere-proximal regions, providing structural constraints crucial for proper genome organization. Loss of heterochromatin relaxes constraints on chromosomes, causing an increase in intra- and inter-chromosomal interactions. Together, our analyses uncover fundamental genome folding principles that drive higher-order chromosome organization crucial for coordinating nuclear functions

Epigenetic control of centromeric Cid/CENP-A levels during spermatogenesis and development

Zentromere sind von größter Wichtigkeit für die richtige Weitergabe der genetischen Information während mitotischer und meiotischer Zellteilungen. Die Identität der Zentromere in Metazoen wird durch epigenetische Mechanismen bestimmt. In Menschen zum Beispiel wurde gezeigt, dass die hochrepetitiven zentromeren DNS-Sequenzen weder genügen noch überhaupt benötigt werden, um das Zentromer zu spezifizieren. Um die Funktion von Proteinen bei der epigenetischen Markierung und Vererbung der Zentromere zu untersuchen, wäre ein effizientes UAS/GAL4- System sehr nützlich, welches für Analysen in der männlichen Keimbahn in Drosophila nach Gen-Überexpression, Gen-Knockdown oder induzierter Proteindegradation geeignet wäre. Daher wurden neuartige Treiberlinien hergestellt, welche GAL4 -Fusionen mittestis-spezifischen Transkriptionsfaktoren exprimieren, in der Hoffnung, dass eine Synergie zwischen den Aktivierungsdomänen von GAL4 und den testis-spezifischen Transkriptionsfaktoren zu einer erhöhten Expression von UASt-Transgenen führen würde. Tatsächlich konnte hierdurch die Effizienz der UASt-Transgene in Spematozyten verbessert werden. Eine der neuen GAL4-Treiberlinien erwies sich bei Experimenten, welche die Funktion von Zentromerproteinen betrafen, als sehr nützlich. Der Hauptteil dieser Arbeit beschreibt Experimente, welche die Weitergabe des Zentromerproteins Cid und der Zentromeridentität während der männlichen Meiose untersuchen. Meine Ergebnisse zeigten, dass sich die Kontrolle der Beladung der Zentromere mit Cid während der männlichen Meiose von der Regulation während der mitotischen Zyklen der frühen Embryogenese unterscheidet. Darüber hinaus wurde gezeigt, dass ein starker Mangel an Cid in Spermien zu einem Versagen der paternalen Zentromerfunktion nach der Befruchtung führt. Paternale Chromosomen, denen Cid am Zentromer fehlte, konnten nicht in die gonomere Spindel der ersten Mitose integriert werden, was zu gynogenetisch haploiden Embryonen führte. Weiterhin wurde nach moderater Depletion von Cid in Spermien beobachtet, dass die paternalen Zentromere in der nächsten Generation nicht die normale Cid-Menge zurückerlangen konnten. Daraus folgere ich, dass Cid in Spermien ein essentieller Bestandteil der epigenetischen Markierung der Zentromere ist. Weiterhin übt das in Spermien vorhandene Cid eine quantitative Kontrolle über die Cid-Menge am Zentromer der paternalen Chromosomen während der Entwicklung der nächsten Generation aus. Summary Centromeres are of paramount importance for faithful propagation of genetic information during mitotic and meiotic divisions. Centromere identity in metazoans is believed to be specified by epigenetic mechanisms. In humans for example, the highly repetitive centromeric DNA has been shown to be neither sufficient nor required for centromere specification. In order to study the role of proteins for epigenetic marking and propagation of centromeres, an efficient UAS/GAL4 system for analyses in the male germline of Drosophila after gene overexpression, knockdown or induced protein degradation would be very helpful. Therefore, novel driver lines expressing GAL4 fused to testis-specific transcription factors were generated in the hope that a synergism between the activation domains of GAL4 and testis-specific transcription factors might result in enhanced UASt transgene expression. Thereby the efficiency of expression of UASt transgenes in spermatocytes could indeed be improved. One of the novel GAL4 driver lines was very useful for experiments concerning centromere protein function. The main part of this thesis describes experiments addressing propagation of the centromere protein Cid and of centromere identity during male meiosis. My results revealed that the control of Cid loading onto centromeres during male meiosis is distinct from the regulation observed during the mitotic cycles of early embryogenesis. Moreover, strong Cid depletion in sperm was shown to result in a failure of paternal centromere function after fertilization. Paternal chromosomes lacking centromeric Cid failed to integrate into the gonomeric spindle of the first mitosis, resulting in gynogenetic haploid embryos. Furthermore, after moderate Cid depletion in sperm, paternal centromeres were found to be unable to re-acquire normal Cid levels in the next generation. Therefore, I conclude that Cid in sperm is an essential component of the epigenetic centromere mark on paternal chromosomes. Moreover, Cid present in sperm centromeres exerts quantitative control over centromeric Cid levels on paternal chromosome throughout development of the next generation

Linear Growth Trajectories, Catch-up Growth, and Its Predictors Among North Indian Small-for-Gestational Age Low Birthweight Infants: A Secondary Data Analysis

Background: Low birthweight small-for-gestational-age (SGA-LBW) (birthweight below the 10th percentile for gestational age; SGA-LBW) infants are at an increased risk of poor postnatal growth outcomes. Linear growth trajectories of SGA-LBW infants are less studied in South Asian settings including India. Objectives: To describe the linear growth trajectories of the SGA-LBW infants compared with appropriate-for-gestational-age LBW (AGA-LBW) infants during the first 6 months of life. In addition, we estimated catch-up growth (ΔLAZ > 0.67) in SGA-LBW infants and their performance against the WHO linear growth velocity cut-offs. Additionally, we studied factors associated with poor catch-up growth in SGA-LBW infants. Methods: The data utilized came from an individually randomized controlled trial that included low birthweight (LBW) infants weighing 1,500–2,250 g at birth. A total of 8,360 LBW infants were included. For comparison between SGA-LBW and AGA-LBW infants, we presented unadjusted and adjusted estimates for mean differences (MDs) or risk ratios (RRs) for the outcomes of length, linear growth velocity, length for age z-score (LAZ) score, and stunting. We estimated the proportion of catch-up growth. Generalized linear models of the Poisson family with log links were used to identify factors associated with poor catch-up growth in SGA-LBW infants. Results: Low birthweight small-for-gestational-age infants had a higher risk of stunting, lower attained length, and a lower LAZ score throughout the first 6 months of life compared with AGA-LBW infants, with differences being maximum at 28 days and minimum at 6 months of age. The linear growth velocity in SGA-LBW infants compared with AGA-LBW infants was significantly lower during the birth–28 day period [MD −0.19, 95% confidence interval (CI): −0.28 to −0.10] and higher during the 3- to 6-month period (MD 0.17, 95% CI: 0.06–0.28). Among the SGA-LBW infants, 55% showed catch-up growth for length at 6 months of age. Lower wealth quintiles, high birth order, home birth, male child, term delivery, non-exclusive breastfeeding, and pneumonia were associated with the higher risk of poor catch-up in linear growth among SGA-LBW infants. Conclusion: Small for gestational age (SGA) status at birth, independent of gestational age, is a determinant of poor postnatal linear growth. Promotion of institutional deliveries, exclusive breastfeeding, and prevention and early treatment of pneumonia may be helpful to improve linear growth in SGA-LBW infants during early infancy.publishedVersio