Molecular basis and evolutionary drivers of endosperm-based hybridization barriers

The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.

Flowering plant reproduction

Flowering plants, also known as angiosperms, emerged approximately 150 to 200 million years ago. Since then, they have undergone rapid and extensive expansion, now encompassing around 90% of all land plant species. The remarkable diversification of this group has been a subject of in-depth investigations, and several evolutionary innovations have been proposed to account for their success. In this primer, we will specifically focus on one such innovation: the advent of seeds containing endosperm.

Helitrons: genomic parasites that generate developmental novelties

Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.

Plant development: How to kill the endosperm

Using molecular markers and genetic analysis of mutant phenotypes, a new study reveals that endosperm elimination in plant seeds is under control of the programmed cell death pathway.

Updated Phylogeny and Protein Structure Predictions Revise the Hypothesis on the Origin of MADS-box Transcription Factors in Land Plants

MADS-box transcription factors (TFs), among the first TFs extensively studied, exhibit a wide distribution across eukaryotes and play diverse functional roles. Varying by domain architecture, MADS-box TFs in land plants are categorized into Type I (M-type) and Type II (MIKC-type). Type I and II genes have been considered orthologous to the SRF and MEF2 genes in animals, respectively, presumably originating from a duplication before the divergence of eukaryotes. Here, we exploited the increasing availability of eukaryotic MADS-box sequences and reassessed their evolution. While supporting the ancient duplication giving rise to SRF- and MEF2-types, we found that Type I and II genes originated from the MEF2-type genes through another duplication in the most recent common ancestor (MRCA) of land plants. Protein structures predicted by AlphaFold2 and OmegaFold support our phylogenetic analyses, with plant Type I and II TFs resembling the MEF2-type structure, rather than SRFs. We hypothesize that the ancestral SRF-type TFs were lost in the MRCA of Archaeplastida (the kingdom Plantae sensu lato). The retained MEF2-type TFs acquired a Keratin-like domain and became MIKC-type before the divergence of Streptophyta. Subsequently in the MRCA of land plants, M-type TFs evolved from a duplicated MIKC-type precursor through loss of the Keratin-like domain, leading to the Type I clade. Both Type I and II TFs expanded and functionally differentiated in concert with the increasing complexity of land plant body architecture. The recruitment of these originally stress-responsive TFs into developmental programs, including those underlying reproduction, may have facilitated the adaptation to the terrestrial environment.

[Diagnostic Imaging during pregnancy of the dog]

Diagnostic imaging represents an important part during modern pregnancy management of the dog. Ultrasound has become the modality of choice for an early pregnancy diagnosis, enabling a verification as early as 17-20 days after LH surge. Furthermore an evaluation of fetal viability and development is possible as well as the depiction of malformations and an early assessment of fetal stress. Doppler imaging may also be of supporting value in this context . Using fetal maturity as well as measurements of fetal and extrafetal structures, a calculation of the gestational age and therefore the time of parturition is achievable. Radiographs of the caudal abdomen enable pregnancy diagnosis from the 43rd day after LH surge onward. In addition, an assessment of fetal size as well as litter size is possible. Both modalities allow for complementary statements concerning possible labor complications and possess supporting value concerning the decision of necessary obstetric intervention and further management in patients with dystocia.

Endosperm cellularization failure induces a dehydration-stress response leading to embryo arrest

The endosperm is a nutritive tissue supporting embryo growth in flowering plants. Most commonly, the endosperm initially develops as a coenocyte (multinucleate cell) and then cellularizes. This process of cellularization is frequently disrupted in hybrid seeds generated by crosses between different flowering plant species or plants that differ in ploidy, resulting in embryo arrest and seed lethality. The reason for embryo arrest upon cellularization failure remains unclear. In this study, we show that triploid Arabidopsis thaliana embryos surrounded by uncellularized endosperm mount an osmotic stress response that is connected to increased levels of abscisic acid (ABA) and enhanced ABA responses. Impairing ABA biosynthesis and signaling aggravated triploid seed abortion, while increasing endogenous ABA levels as well as the exogenous application of ABA-induced endosperm cellularization and suppressed embryo growth arrest. Taking these results together, we propose that endosperm cellularization is required to establish dehydration tolerance in the developing embryo, ensuring its survival during seed maturation.

Meiocyte size is a determining factor for unreduced gamete formation in Arabidopsis thaliana

Polyploidy, the presence of more than two sets of chromosomes within a cell, is a widespread phenomenon in plants. The main route to polyploidy is considered through the production of unreduced gametes that are formed as a consequence of meiotic defects. Nevertheless, for reasons poorly understood, the frequency of unreduced gamete formation differs substantially among different plant species. The previously identified meiotic mutant jason (jas) in Arabidopsis thaliana forms about 60% diploid (2n) pollen. JAS is required to maintain an organelle band as a physical barrier between the two meiotic spindles, preventing previously separated chromosome groups from uniting into a single cell. In this study, we characterized the jas suppressor mutant telamon (tel) that restored the production of haploid pollen in the jas background. The tel mutant did not restore the organelle band, but enlarged the size of male jas tel meiocytes, suggesting that enlarged meiocytes can bypass the requirement of the organelle band. Consistently, enlarged meiocytes generated by a tetraploid jas mutant formed reduced gametes. The results reveal that meiocyte size impacts chromosome segregation in meiosis II, suggesting an alternative way to maintain the ploidy stability in meiosis during evolution.

Genomic imprinting regulates establishment and release of seed dormancy

Seed dormancy enables plant seeds to time germination until environmental conditions become favorable for seedling survival. This trait has high adaptive value and is of great agricultural relevance. The endosperm is a reproductive tissue formed after fertilization that in addition to support embryo growth has major roles in establishing seed dormancy. Many genes adopt parent-of-origin specific expression patterns in the endosperm, a phenomenon that has been termed genomic imprinting. Imprinted genes are targeted by epigenetic mechanisms acting before and after fertilization. Recent studies revealed that imprinted genes are involved in establishing seed dormancy, highlighting a new mechanism of parental control over this adaptive trait. Here, we review the regulatory mechanisms establishing genomic imprinting and their effect on seed dormancy.

New Constraint on the Local Relic Neutrino Background Overdensity with the First KATRIN Data Runs

We report on the direct search for cosmic relic neutrinos using data acquired during the first two science campaigns of the KATRIN experiment in 2019. Beta-decay electrons from a high-purity molecular tritium gas source are analyzed by a high-resolution MAC-E filter around the end point at 18.57 keV. The analysis is sensitive to a local relic neutrino overdensity ratio of η<9.7×10^{10}/α (1.1×10^{11}/α) at a 90% (95%) confidence level with α=1 (0.5) for Majorana (Dirac) neutrinos. A fit of the integrated electron spectrum over a narrow interval around the end point accounting for relic neutrino captures in the tritium source reveals no significant overdensity. This work improves the results obtained by the previous neutrino mass experiments at Los Alamos and Troitsk. We furthermore update the projected final sensitivity of the KATRIN experiment to η<1×10^{10}/α at 90% confidence level, by relying on updated operational conditions.

Brachycephaly in French bulldogs and pugs is associated with narrow ear canals

BACKGROUND

Brachycephalic dog breeds have multiple skull malformations which may lead to anatomical changes in the external auditory canal. It is our frequent observation that in the otoscopic examination of the external ear in these breeds we are unable to visualise the tympanic membrane as a consequence of extreme narrowing of the proximal ear canal. Additionally brachycephalic dogs reportedly are predisposed to otitis externa (OE) and otitis media.

OBJECTIVES

To characterizse the transition of the cartilaginous ear canal to the bony meatus acusticus externus using computed tomography (CT) and to investigate a possible association with OE in brachycephalic dogs.

MATERIALS AND METHODS

Seventy-five client-owned dogs [pugs (n = 20), French bulldogs (n = 55)] were included and assessed for OE using an owner questionnaire and otoscopic and cytological examinations. In dorsal plane CT scans, the diameter of the porus acusticus externus was measured using novel methodology. The results were compared with a normocephalic control group without preexisting otological disorders.

RESULTS

Brachycephalic dogs had a significantly smaller porus acusticus externus diameter (2.6 mm) than normocephalic dogs (5.0 mm). Of the brachycephalic dogs, 32% had OE yet this was not statistically significantly related to the diameter of the porus acusticus externus. Middle ear effusion (44%) and narrowing of the external ear canal (82.6%) were significantly more frequent in brachycephalic dogs. Only five of 150 eardrums could be visualised otoscopically.

CONCLUSIONS AND CLINICAL RELEVANCE

Malformation of the porus acusticus externus causes severe stenosis of the proximal ear canal in brachycephalic dogs. A connection between stenosis of the external auditory canal and OE could not be confirmed.

Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis

The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.

The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation

Animal and plant microRNAs (miRNAs) are essential for the spatio-temporal regulation of development. Together with this role, plant miRNAs have been proposed to target transposable elements (TEs) and stimulate the production of epigenetically active small interfering RNAs. This activity is evident in the plant male gamete containing structure, the male gametophyte or pollen grain. How the dual role of plant miRNAs, regulating both genes and TEs, is integrated during pollen development and which mRNAs are regulated by miRNAs in this cell type at a genome-wide scale are unknown. Here, we provide a detailed analysis of miRNA dynamics and activity during pollen development in Arabidopsis thaliana using small RNA and degradome parallel analysis of RNA end high-throughput sequencing. Furthermore, we uncover miRNAs loaded into the two main active Argonaute (AGO) proteins in the uninuclear and mature pollen grain, AGO1 and AGO5. Our results indicate that the developmental progression from microspore to mature pollen grain is characterized by a transition from miRNAs targeting developmental genes to miRNAs regulating TE activity.

Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors

MADS-box transcription factors (TFs) are present in nearly all major eukaryotic groups. They are divided into Type I and Type II that differ in domain structure, functional roles, and rates of evolution. In flowering plants, major evolutionary innovations like flowers, ovules, and fruits have been closely connected to Type II MADS-box TFs. The role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Here, we show that the formation of angiosperm-specific Type I MADS-box clades of Mγ and Mγ-interacting Mα genes (Mα*) can be tracked back to the ancestor of all angiosperms. Angiosperm-specific Mγ and Mα* genes were preferentially expressed in the endosperm, consistent with their proposed function as heterodimers in the angiosperm-specific embryo nourishing endosperm tissue. We propose that duplication and diversification of Type I MADS genes underpin the evolution of the endosperm, a developmental innovation closely connected to the origin and success of angiosperms.

3T MRI characteristics of the palatine tonsil in brachycephalic dogs

OBJECTIVE

Investigation of the MRI characteristics of the palatine tonsil in brachycephalic dogs in 3T high-field system.

MATERIAL AND METHODS

Eighty-five brachycephalic dogs and 37 normocephalic dogs were divided into five groups: group 1 French bulldogs (FBs) with neurological clinical signs (n = 37), group 2 FBs with brachycephalic obstructive airway syndrome (BOAS) (n = 22), group 3 pugs with neurological clinical signs (n = 17), group 4 pugs with BOAS (n = 9) and group 5 normocephalic dogs (n = 37). Cross-sectional area and volume measurements were performed, and tonsillar margination and contour, shape, signal intensity and homogeneity/heterogeneity of the palatine tonsils were evaluated and compared.

RESULTS

Cross-sectional area and volume measurements of the tonsils showed no significant differences between brachycephalic and normocephalic dogs with the exception of the dogs of group 2 (FB BOAS), which showed relatively high volume and large cross-sectional area in comparison to other groups. In 87% of the brachycephalic animals, the tonsils were well defined. A smooth contour was detectable in 91.8% and a rounded shape in 94.7% of brachycephalic dogs. Signal intensity was assessed as hyperintense in relation to the musculature and iso- to hyperintense to the soft palate. Heterogeneous appearance was described in 86.9% of the brachycephalic animals.

CONCLUSIONS

The MRI characteristics of the tonsils of brachycephalic dogs do not differ considerably from those of normocephalic dogs. In FBs with distinct clinical signs of obstructive airway syndrome, increase in cross-sectional area and volume of the tonsils was detected.

MRI diagnosis of spontaneous intraventricular tension-pneumocephalus in a 10-month-old male Saarloos Wolfdog

A 10-month-old male Saarloos Wolfdog was presented with a history of multiple neurologic deficits that had acutely progressed. Neurologic examination findings localized signs to the cerebrum and brainstem. Magnetic resonance imaging revealed markedly enlarged and gas-filled lateral ventricles with a mass effect leading to cerebellar herniation. A right-sided defect of the cribriform plate with a dysplastic ethmoturbinate was identified as the inlet of air and origin of the intraventricular tension pneumocephalus. Surgical findings were consistent with a ruptured, congenital, nasal meningocele.

Neue Terminologie für Sprachentwicklungsstörungen?

Hintergrund

Sprachtherapeutisch-linguistische Fachkreise empfehlen die Anpassung einer von einem internationalen Konsortium empfohlenen Änderung der Nomenklatur für Sprachstörungen im Kindesalter, insbesondere für Sprachentwicklungsstörungen (SES), auch für den deutschsprachigen Raum.

Fragestellung

Ist eine solche Änderung in der Terminologie aus ärztlicher und psychologischer Sicht sinnvoll?

Material und Methode

Kritische Abwägung der Argumente für und gegen eine Nomenklaturänderung aus medizinischer und psychologischer Sicht eines Fachgesellschaften- und Leitliniengremiums.

Ergebnisse

Die ICD-10-GM (Internationale statistische Klassifikation der Krankheiten und verwandter Gesundheitsprobleme, 10. Revision, German Modification) und eine S2k-Leitlinie unterteilen SES in umschriebene SES (USES) und SES assoziiert mit anderen Erkrankungen (Komorbiditäten). Die USES- wie auch die künftige SES-Definition der ICD-11 (International Classification of Diseases 11th Revision) fordern den Ausschluss von Sinnesbehinderungen, neurologischen Erkrankungen und einer bedeutsamen intellektuellen Einschränkung. Diese Definition erscheint weit genug, um leichtere nonverbale Einschränkungen einzuschließen, birgt nicht die Gefahr, Kindern Sprach- und weitere Therapien vorzuenthalten und erkennt das ICD(International Classification of Disease)-Kriterium, nach dem der Sprachentwicklungsstand eines Kindes bedeutsam unter der Altersnorm und unterhalb des seinem Intelligenzalter angemessenen Niveaus liegen soll, an. Die intendierte Ersetzung des Komorbiditäten-Begriffs durch verursachende Faktoren, Risikofaktoren und Begleiterscheinungen könnte die Unterlassung einer dezidierten medizinischen Differenzialdiagnostik bedeuten.

Schlussfolgerungen

Die vorgeschlagene Terminologie birgt die Gefahr, ätiologisch bedeutsame Klassifikationen und differenzialdiagnostische Grenzen zu verwischen und auf wertvolles ärztliches und psychologisches Fachwissen in Diagnostik und Therapie sprachlicher Störungen im Kindesalter zu verzichten.

H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

BACKGROUND

Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression. The deposition of H3 lysine 27 tri-methylation (H3K27me3) by PRC2 is known to be required for transcriptional repression, whereas the contribution of H2A ubiquitination (H2Aub) in the Polycomb repressive system remains unclear in plants.

RESULTS

We directly test the requirement of H2Aub for gene regulation in Marchantia polymorpha by generating point mutations in H2A that prevent ubiquitination by PRC1. These mutants show reduced H3K27me3 levels on the same target sites as mutants defective in PRC1 subunits MpBMI1 and the homolog MpBMI1L, revealing that PRC1-catalyzed H2Aub is essential for Polycomb system function. Furthermore, by comparing transcriptome data between mutants in MpH2A and MpBMI1/1L, we demonstrate that H2Aub contributes to the PRC1-mediated transcriptional level of genes and transposable elements.

CONCLUSION

Together, our data demonstrates that H2Aub plays a direct role in H3K27me3 deposition and is required for PRC1-mediated transcriptional changes in both genes and transposable elements in Marchantia.

Combinations of maternal-specific repressive epigenetic marks in the endosperm control seed dormancy

Polycomb Repressive Complex 2 (PRC2)-mediated trimethylation of histone H3 on lysine 27 (H3K27me3) and methylation of histone 3 on lysine 9 (H3K9me) are two repressive epigenetic modifications that are typically localized in distinct regions of the genome. For reasons unknown, however, they co-occur in some organisms and special tissue types. In this study, we show that maternal alleles marked by H3K27me3 in the Arabidopsis endosperm were targeted by the H3K27me3 demethylase REF6 and became activated during germination. In contrast, maternal alleles marked by H3K27me3, H3K9me2, and CHG methylation (CHGm) are likely to be protected from REF6 targeting and remained silenced. Our study unveils that combinations of different repressive epigenetic modifications time a key adaptive trait by modulating access of REF6.

On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae)

Polyploidy, or whole-genome duplication, is a common speciation mechanism in plants. An important barrier to polyploid establishment is a lack of compatible mates. Because self-compatibility alleviates this problem, it has long been hypothesized that there should be an association between polyploidy and self-compatibility (SC), but empirical support for this prediction is mixed. Here, we investigate whether the molecular makeup of the Brassicaceae self-incompatibility (SI) system, and specifically dominance relationships among S-haplotypes mediated by small RNAs, could facilitate loss of SI in allopolyploid crucifers. We focus on the allotetraploid species Capsella bursa-pastoris, which formed ~300 kya by hybridization and whole-genome duplication involving progenitors from the lineages of Capsella orientalis and Capsella grandiflora. We conduct targeted long-read sequencing to assemble and analyze eight full-length S-locus haplotypes, representing both homeologous subgenomes of C. bursa-pastoris. We further analyze small RNA (sRNA) sequencing data from flower buds to identify candidate dominance modifiers. We find that C. orientalis-derived S-haplotypes of C. bursa-pastoris harbor truncated versions of the male SI specificity gene SCR and express a conserved sRNA-based candidate dominance modifier with a target in the C. grandiflora-derived S-haplotype. These results suggest that pollen-level dominance may have facilitated loss of SI in C. bursa-pastoris. Finally, we demonstrate that spontaneous somatic tetraploidization after a wide cross between C. orientalis and C. grandiflora can result in production of self-compatible tetraploid offspring. We discuss the implications of this finding on the mode of formation of this widespread weed.

INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis

Higher-order chromatin structure undergoes striking changes in response to various developmental and environmental signals, causing distinct cell types to adopt specific chromatin organization. High throughput chromatin conformation capture (Hi-C) allows studying higher-order chromatin structure; however, this technique requires substantial amounts of starting material, which has limited the establishment of cell type-specific higher-order chromatin structure in plants. To overcome this limitation, we established a protocol that is applicable to a limited amount of nuclei by combining the INTACT (isolation of nuclei tagged in specific cell types) method and Hi-C (INT-Hi-C). Using this INT-Hi-C protocol, we generated Hi-C data from INTACT purified endosperm and leaf nuclei. Our INT-Hi-C data from leaf accurately reiterated chromatin interaction patterns derived from conventional leaf Hi-C data. We found that the higher-order chromatin organization of mixed leaf tissues and endosperm differs and that DNA methylation and repressive histone marks positively correlate with the chromatin compaction level. We furthermore found that self-looped interacting genes have increased expression in leaves and endosperm and that interacting intergenic regions negatively impact on gene expression in the endosperm. Last, we identified several imprinted genes involved in long-range and trans interactions exclusively in endosperm. Our study provides evidence that the endosperm adopts a distinct higher-order chromatin structure that differs from other cell types in plants and that chromatin interactions influence transcriptional activity.

Sexual, bladder and bowel function following different minimally invasive techniques of radical hysterectomy in patients with early-stage cervical cancer

Purpose

Despite the establishment of radical surgery for therapy of cervical cancer, data on quality of life and patient-reported outcomes are scarce. The aim of this retrospective cohort study was to evaluate bladder, bowel and sexual function in women who underwent minimally invasive surgery for early-stage cervical cancer.

Methods

From 2007–2013, 261 women underwent laparoscopically assisted radical vaginal hysterectomy (LARVH = 45), vaginally assisted laparoscopic or robotic radical hysterectomy (VALRRH = 61) or laparoscopic total mesometrial resection (TMMR = 25) and 131 of them completed the validated German version of the Australian Pelvic Floor Questionnaire (PFQ). Results were compared with controls recruited from gynecological clinics (n = 24) and with urogynecological patients (n = 63).

Results

Groups were similar regarding age, BMI and parity. The TMMR group had significantly shorter median follow-up (16 months versus 70 and 36 months). Postoperatively, deterioration of bladder function was reported by 70%, 57% and 44% in the LARVH, VARRVH and TMMR groups, respectively (p = 0.734). Bowel function was significantly worse after TMMR with a higher deterioration rate in 72 versus 43% (LARVH) and 47% (VARRVH) with a correspondingly higher bowel dysfunction score of 2.9 versus 1.5 and 1.8, respectively and 1.8 in urogynaecological patients. Sexual dysfunction was common in all surgical groups. 38% considered their vagina too short which was significantly associated with deep dyspareunia.

Compared with controls, surgical groups had significantly increased PFQ scores.

Conclusion

Pelvic floor dysfunction commonly deteriorates and negatively impacts on quality of life after minimally invasive radical hysterectomy, especially bowel function after TMMR. Pelvic floor symptoms should routinely be addressed pre- and postoperatively.

Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis

BACKGROUND

Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. In Arabidopsis, loss of function of NRPD1, encoding the largest subunit of the plant-specific RNA polymerase IV (Pol IV), can suppress the triploid block. Pol IV generates short RNAs required to guide de novo methylation in the RNA-directed DNA methylation (RdDM) pathway. Recent work suggests that suppression of the triploid block by mutants in RdDM components differs, depending on whether the diploid pollen is derived from tetraploid plants or from the omission in second division 1 (osd1) mutant. This study aims to understand this difference.

RESULTS

In this study, we find that the ability of mutants in the RdDM pathway to suppress the triploid block depends on their degree of inbreeding. While first homozygous generation mutants in RdDM components NRPD1, RDR2, NRPE1, and DRM2 have weak or no ability to rescue the triploid block, they are able to suppress the triploid block with successive generations of inbreeding. Inbreeding of nrpd1 was connected with a transgenerational loss of non-CG DNA methylation on sites jointly regulated by CHROMOMETHYLASES 2 and 3.

CONCLUSIONS

Our data reveal that loss of RdDM function differs in its effect in early and late generations, which has important implications when interpreting the effect of RdDM mutants.

Polycomb Repressive Complex 2 and KRYPTONITE regulate pathogen-induced programmed cell death in Arabidopsis

The Polycomb Repressive Complex 2 (PRC2) is well-known for its role in controlling developmental transitions by suppressing the premature expression of key developmental regulators. Previous work revealed that PRC2 also controls the onset of senescence, a form of developmental programmed cell death (PCD) in plants. Whether the induction of PCD in response to stress is similarly suppressed by the PRC2 remained largely unknown. In this study, we explored whether PCD triggered in response to immunity- and disease-promoting pathogen effectors is associated with changes in the distribution of the PRC2-mediated histone H3 lysine 27 trimethylation (H3K27me3) modification in Arabidopsis thaliana. We furthermore tested the distribution of the heterochromatic histone mark H3K9me2, which is established, to a large extent, by the H3K9 methyltransferase KRYPTONITE, and occupies chromatin regions generally not targeted by PRC2. We report that effector-induced PCD caused major changes in the distribution of both repressive epigenetic modifications and that both modifications have a regulatory role and impact on the onset of PCD during pathogen infection. Our work highlights that the transition to pathogen-induced PCD is epigenetically controlled, revealing striking similarities to developmental PCD.

Postzygotic reproductive isolation established in the endosperm: mechanisms, drivers and relevance

The endosperm is a developmental innovation of angiosperms that supports embryo growth and germination. Aside from this essential reproductive function, the endosperm fuels angiosperm evolution by rapidly establishing reproductive barriers between incipient species. Specifically, the endosperm prevents hybridization of newly formed polyploids with their non-polyploid progenitors, a phenomenon termed the triploid block. Furthermore, recently diverged diploid species are frequently reproductively isolated by endosperm-based hybridization barriers. Current genetic approaches have revealed a prominent role for epigenetic processes establishing these barriers. In particular, imprinted genes, which are expressed in a parent-of-origin-specific manner, underpin the interploidy barrier in the model species Arabidopsis. We will discuss the mechanisms establishing hybridization barriers in the endosperm, the driving forces for these barriers and their impact for angiosperm evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm

Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTL for the underlying cause of hybrid incompatibility in Capsella identified three QTL that were close to pericentromeric regions. We investigated whether there are specific changes in heterochromatin associated with interspecific hybridizations and found a strong reduction of chromatin condensation in the endosperm, connected with a strong loss of CHG and CHH methylation and random loss of a single chromosome. Consistent with reduced DNA methylation in the hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions, suggesting that reduced DNA methylation allows access of transcription factors to targets located in heterochromatic regions. Since the identified QTL were also associated with pericentromeric regions, we propose that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.

Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress

Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.

Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce

Epigenetic reprogramming during germ cell formation is essential to gain pluripotency and thus embryogenic potential. The histone modification H3K27me3, which is catalysed by the Polycomb repressive complex 2 (PRC2), regulates important developmental processes in both plants and animals, and defects in PRC2 components cause pleiotropic developmental abnormalities. Nevertheless, the role of H3K27me3 in determining embryogenic potential in gymnosperms is still elusive. To address this, we generated H3K27me3 profiles of Norway spruce (Picea abies) embryonic callus and non-embryogenic callus using CUT&RUN, which is a powerful method for chromatin profiling. Here, we show that H3K27me3 mainly accumulated in genic regions in the Norway spruce genome, similarly to what is observed in other plant species. Interestingly, H3K27me3 levels in embryonic callus were much lower than those in the other examined tissues, but markedly increased upon embryo induction. These results show that H3K27me3 levels are associated with the embryogenic potential of a given tissue, and that the early phase of somatic embryogenesis is accompanied by changes in H3K27me3 levels. Thus, our study provides novel insights into the role of this epigenetic mark in spruce embryogenesis and reinforces the importance of PRC2 as a key regulator of cell fate determination across different plant species.

Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor

Allosteric communication within proteins is a hallmark of biochemical signaling, but the dynamic transmission pathways remain poorly characterized. We combined NMR spectroscopy and surface plasmon resonance to reveal these pathways and quantify their energetics in the glucocorticoid receptor, a transcriptional regulator controlling development, metabolism, and immune response. Our results delineate a dynamic communication network of residues linking the ligand-binding pocket to the activation function-2 interface, where helix 12, a switch for transcriptional activation, exhibits ligand- and coregulator-dependent dynamics coupled to graded activation. The allosteric free energy responds to variations in ligand structure: subtle changes gradually tune allostery while preserving the transmission pathway, whereas substitution of the entire pharmacophore leads to divergent allosteric control by apparently rewiring the communication network. Our results provide key insights that should aid in the design of mechanistically differentiated ligands.

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis

BACKGROUND

Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and subsequent trimethylation of lysine 27 of histone 3 (H3K27me3). Previous work proposed that H2Aub1 removal by the ubiquitin-specific proteases 12 and 13 (UBP12 and UBP13) is part of the repressive PRC1&2 system, but its functional role remains elusive.

RESULTS

We show that UBP12 and UBP13 work together with PRC1, PRC2, and EMF1 to repress genes involved in stimulus response. We find that PRC1-mediated H2Aub1 is associated with gene responsiveness, and its repressive function requires PRC2 recruitment. We further show that the requirement of PRC1 for PRC2 recruitment depends on the initial expression status of genes. Lastly, we demonstrate that removal of H2Aub1 by UBP12/13 prevents loss of H3K27me3, consistent with our finding that the H3K27me3 demethylase REF6 is positively associated with H2Aub1.

CONCLUSIONS

Our data allow us to propose a model in which deposition of H2Aub1 permits genes to switch between repression and activation by H3K27me3 deposition and removal. Removal of H2Aub1 by UBP12/13 is required to achieve stable PRC2-mediated repression.

Polymerase IV Plays a Crucial Role in Pollen Development in Capsella

In Arabidopsis (Arabidopsis thaliana), DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA transcripts. These transcripts are processed by DICER-LIKE3 into 24-nucleotide small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nucleotide epigenetically activated siRNAs, which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernible pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV, in the Brassicaceae species Capsella (Capsella rubella), caused postmeiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nucleotide and 24-nucleotide siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella compared with Arabidopsis, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.

DFTB+, a software package for efficient approximate density functional theory based atomistic simulations

DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.

Genomic imprinting in plants-revisiting existing models

In this review, Batista and Köhler revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting.

Genomic imprinting is an epigenetic phenomenon leading to parentally biased gene expression. Throughout the years, extensive efforts have been made to characterize the epigenetic marks underlying imprinting in animals and plants. As a result, DNA methylation asymmetries between parental genomes emerged as the primary factor controlling the imprinting status of many genes. Nevertheless, the data accumulated so far suggest that this process cannot solely explain the imprinting of all genes. In this review, we revisit the current models explaining imprinting regulation in plants, and discuss novel regulatory mechanisms that could function independently of parental DNA methylation asymmetries in the establishment of imprinting.

Dark-Induced Senescence Causes Localized Changes in DNA Methylation

Senescence occurs in a programmed manner to dismantle the vegetative tissues and redirect nutrients towards metabolic pathways supporting reproductive success. External factors can trigger the senescence program as an adaptive strategy, indicating that this terminal program is controlled at different levels. It has been proposed that epigenetic factors accompany the reprogramming of the senescent genome; however, the mechanism and extent of this reprogramming remain unknown. Using bisulphite conversion followed by sequencing, we assessed changes in the methylome of senescent Arabidopsis (Arabidopsis thaliana) leaves induced by darkness and monitored their effect on gene and transposable element (TE) expression with transcriptome sequencing. Upon dark-induced senescence, genes controlling chromatin silencing were collectively down-regulated. As a consequence, the silencing of TEs was impaired, causing in particular young TEs to become preferentially reactivated. In parallel, heterochromatin at chromocenters was decondensed. Despite the disruption of the chromatin maintenance network, the global DNA methylation landscape remained highly stable, with localized changes mainly restricted to CHH methylation. Together, our data show that the terminal stage of plant life is accompanied by global changes in chromatin structure but only localized changes in DNA methylation, adding another example of the dynamics of DNA methylation during plant development.

Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce

BACKGROUND

Small RNAs (sRNAs) are regulatory molecules impacting on gene expression and transposon activity. MicroRNAs (miRNAs) are responsible for tissue-specific and environmentally-induced gene repression. Short interfering RNAs (siRNA) are constitutively involved in transposon silencing across different type of tissues. The male gametophyte in angiosperms has a unique set of sRNAs compared to vegetative tissues, including phased siRNAs from intergenic or genic regions, or epigenetically activated siRNAs. This is contrasted by a lack of knowledge about the sRNA profile of the male gametophyte of gymnosperms.

RESULTS

Here, we isolated mature pollen from male cones of Norway spruce and investigated its sRNA profiles. While 21-nt sRNAs is the major size class of sRNAs in needles, in pollen 21-nt and 24-nt sRNAs are the most abundant size classes. Although the 24-nt sRNAs were exclusively derived from TEs in pollen, both 21-nt and 24-nt sRNAs were associated with TEs. We also investigated sRNAs from somatic embryonic callus, which has been reported to contain 24-nt sRNAs. Our data show that the 24-nt sRNA profiles are tissue-specific and differ between pollen and cell culture.

CONCLUSION

Our data reveal that gymnosperm pollen, like angiosperm pollen, has a unique sRNA profile, differing from vegetative leaf tissue. Thus, our results reveal that angiosperm and gymnosperm pollen produce new size classes not present in vegetative tissues; while in angiosperm pollen 21-nt sRNAs are generated, in the gymnosperm Norway spruce 24-nt sRNAs are generated. The tissue-specific production of distinct TE-derived sRNAs in angiosperms and gymnosperms provides insights into the diversification process of sRNAs in TE silencing pathways between the two groups of seed plants.

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

Improved Upper Limit on the Neutrino Mass from a Direct Kinematic Method by KATRIN

We report on the neutrino mass measurement result from the first four-week science run of the Karlsruhe Tritium Neutrino experiment KATRIN in spring 2019. Beta-decay electrons from a high-purity gaseous molecular tritium source are energy analyzed by a high-resolution MAC-E filter. A fit of the integrated electron spectrum over a narrow interval around the kinematic end point at 18.57 keV gives an effective neutrino mass square value of (-1.0_{-1.1}^{+0.9})  eV^{2}. From this, we derive an upper limit of 1.1 eV (90% confidence level) on the absolute mass scale of neutrinos. This value coincides with the KATRIN sensitivity. It improves upon previous mass limits from kinematic measurements by almost a factor of 2 and provides model-independent input to cosmological studies of structure formation.

[Evaluation of the accuracy of volume navigation of sonography and computed tomography using a phantom]

BACKGROUND AND OBJECTIVE

In case of superimpositions of gas in the gastrointestinal tract or the ribs, tissue changes well detectable on computed tomography (CT) cannot be identified sonographically in a number of cases. Combining ultrasonography and CT provides enhanced information compared to sole sonography and volume navigation may be used as an effective tool. Tissue samples easily and safely obtained under sonographic guidance are often necessary to confirm the diagnosis of a suspicious focus. In these cases, the spatial fusion of CT and sonography may also be employed for improved visualization of foci by eliminating superimposition of sonographic images which is a limitation of ultrasound. This study investigated the potential benefit and improved informative value of the fusion of CT and sonography in case of superimpositions and aimed at determining the registration method with the best accuracy.

MATERIALS AND METHODS

Sixteen models (10 models with peas [low contrast], 6 models with wooden spheres [high contrast] as round structures) were created. These models were examined by computed tomography and fused using 3 volume navigation protocols. Subsequently, volume-guided sonography was performed. The deviation of the specimens was measured.

RESULTS

In total, 1026 measurements of the pea models and 648 measurements of the wooden sphere models were carried out. A fusion accuracy of 100 % was observed in 9.9 % (102/1026) resp. 9.9 % (64/648) of the models. In 85.4 % (876/1026) resp. 94.1 % (610/648) the deviation was < 5 mm and in 98.1 % (1006/1026) resp. 99.4 % (644/648) it was < 10 mm. The registration protocol in which all reference points were used for spatial fusion proved to be the most accurate CONCLUSION: The registration protocols for volume-guided ultrasound have sufficient biopsy accuracy to merge identical sites and provide the basis for improved volume-navigated biopsy sampling.

Genetic basis and timing of a major mating system shift in Capsella

A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.

[Contrast-enhanced ultrasound at a rare bilateral renal carcinoma with secondary inflammation and necrosis in a cat]

A 17-year-old male neutered domestic short hair cat was presented because of anorexia. The clinical examination revealed no abnormalities. Using sonography, mainly hypoechoic mass lesions at the level of the cortex and capsule were detected in both kidneys. The severity of the renal lesions could be clearly demonstrated using contrast-enhanced ultrasound and contrast-enhanced computed tomography. Under general anesthesia, fine needle aspirations of the lesions were taken. Part of the lesions were sampled from dorsal, an unusual practice for small animal medicine. Cytology revealed a bilateral renal carcinoma with secondary inflammation and necrosis. The cat improved under medical symptomatic treatment, but was euthanized 2 weeks later.

Implementation of multidrug-resistant tuberculosis (MDR-TB) treatment in Gabon: lessons learnt from the field

PURPOSE

Since May 2016, WHO recommended a 9-12 month short-treatment regimen for multidrug-resistant tuberculosis (MDR-TB) treatment known as the 'Bangladesh Regimen'. However, limited data exist on the appropriateness thereof, and its implementation in low- and middle-income countries (LMIC). We report here on the pilot phase of the evaluation of the Bangladesh regimen in Gabon, prior to its endorsement by the WHO.

METHODS

This ongoing observational study started in September 2015. Intensive training of hospital health workers as well as community information and education were conducted. GeneXpert-confirmed MDR-TB patients received the second-line anti-tuberculosis drugs (4KmMfxPtoHCfzEZ/5MfxCfzEZ). Sputum smears and cultures were done monthly. Adverse events were monitored daily.

RESULTS

Eleven patients have been treated for MDR-TB piloting the short regimen. All were HIV-negative and presented in poor health with extensive pulmonary lesions. The overall sputum culture conversion rate was 64% after 4 months of treatment. Three patients developed marked hearing loss; one a transient cutaneous rash. Of 11 patients in our continuous care, 7 (63.6%) significantly improved clinically and bacteriologically. One (9.1%) patient experienced a treatment failure, two (18.2%) died, and one (9.1%) was lost to follow up.

CONCLUSIONS

Our pioneering data on systematic MDR-TB treatment in Gabon, with currently almost total absence of resistance against the second-line drugs, demonstrate that a 9-month regimen has the capacity to facilitate early culture negativity and sustained clinical improvement. Close adverse events monitoring and continuous care are vital to success.

Endosperm-specific transcriptome analysis by applying the INTACT system

KEY MESSAGE

We report the adaptation of the INTACT method for RNA-sequencing in the endosperm and demonstrate its feasibility for allele-specific expression analysis. Tissue-specific transcriptome analyses provide important insights into the developmental programs of defined cell types. The isolation of nuclei tagged in specific cell types (INTACT) is a versatile method that allows to isolate highly pure nuclei from defined tissue types that can be used for several downstream applications. Here, we describe the adaptation of INTACT from endosperm nuclei for high-throughput RNA-sequencing. By analyzing the ratio of parental reads and tissue-specific gene expression in the endosperm, we could assess the contamination level of our samples. Based on this analysis, we estimate that in most of the samples the contamination level is lower than in previously published datasets. We further show that the nuclear transcriptome and total transcriptome of the endosperm are well correlated. Together, our data show that INTACT of the endosperm is a reliable methodology for endosperm-specific transcriptome analysis that overcomes the limitation of time-consuming manual endosperm dissection that is connected with high levels of maternal tissue contamination. INTACT does not rely on expensive equipment and can be set up in every standard molecular biology laboratory, making it the method of choice for future molecular studies of the endosperm.

Auxin regulates endosperm cellularization in Arabidopsis

Batista et al. show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest.

The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms, endosperm development starts as a syncytium, in which nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species, and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization, and thereby uncovered a central role of auxin in establishing hybridization barriers in plants.

Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

BACKGROUND

Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.

RESULTS

In this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles, we are able to predict known PEGs at high accuracy and identify several new PEGs that we confirm using INTACT-based transcriptomes generated in this study.

CONCLUSIONS

The presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows prediction of genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting.

Inflammatory and regulatory CCL and CXCL chemokine and cytokine cellular responses in patients with patent Mansonella perstans filariasis

Mansonella perstans (Mp) filariasis is present in large populations in sub-Saharan Africa, and to what extent patent Mp infection modulates the expression of immunity in patients, notably their cellular cytokine and chemokine response profile, remains not well known. We studied the spontaneous and inducible cellular production of chemokines (C-X-C motif) ligand 9 (CXCL9) [monokine induced by interferon (IFN)-γ (MIG)], CXCL-10 [inducible protein (IP)-10], chemokine (C-C motif) ligand 24 (CCL24) (eotaxin-2), CCL22 [macrophage-derived chemokine (MDC)], CCL13 [monocyte chemotactic protein-4 (MCP-4)], CCL18 [pulmonary and activation-regulated chemokine (PARC)], CCL17 [thymus- and activation-regulated chemokine (TARC)] and interleukin (IL)-27 in mansonelliasis patients (Mp-PAT) and mansonelliasis-free controls (CTRL). Freshly isolated peripheral mononuclear blood cells (PBMC) were stimulated with helminth, protozoan and bacterial antigens and mitogen [phytohaemagglutinin (PHA)]. PBMC from Mp-PAT produced spontaneously (without antigen stimulation) significantly higher levels of eotaxin-2, IL-27, IL-8, MCP-4 and MDC than cells from CTRL, while IFN-γ-IP-10 was lower in Mp-PAT. Helminth antigens activated IL-27 and MCP-4 only in CTRL, while Ascaris antigen, Onchocerca antigen, Schistosoma antigen, Entamoeba antigen, Streptococcus antigen, Mycobacteria antigen and PHA stimulated MIG release in CTRL and Mp-PAT. Notably, Entamoeba antigen and PHA strongly depressed (P < 0·0001) eotaxin-2 (CCL24) production in both study groups. Multiple regression analyses disclosed in Mp-PAT and CTRL dissimilar cellular chemokine and cytokine production levels being higher in Mp-PAT for CCL24, IL-27, IL-8, MCP-4, MDC and PARC (for all P < 0·0001), at baseline (P < 0·0001), in response to Entamoeba histolytica strain HM1 antigen (EhAg) (P < 0·0001), Onchocerca volvulus adult worm-derived antigen (OvAg) (P = 0·005), PHA (P < 0·0001) and purified protein derivative (PPD) (P < 0·0001) stimulation. In Mp-PAT with hookworm co-infection, the cellular chemokine production of CXCL10 (IP-10) was diminished. In summary, the chemokine and cytokine responses in Mp-PAT were in general not depressed, PBMC from Mp-PAT produced spontaneously and selectively inducible inflammatory and regulatory chemokines and cytokines at higher levels than CTRL and such diverse and distinctive reactivity supports that patent M. perstans infection will not polarize innate and adaptive cellular immune responsiveness in patients.