Vibronic Coupling Drives the Ultrafast Internal Conversion in a Functionalized Free-Base Porphyrin.

Internal conversion (IC) is a common radiationless transition in polyatomic molecules. Theory predicts that molecular vibrations assist IC between excited states, and ultrafast experiments can provide insight into their structure-function relationship. Here we elucidate the dynamics of the vibrational modes driving the IC process within the Q band of a functionalized porphyrin molecule. Through a combination of ultrafast multidimensional spectroscopies and theoretical modeling, we observe a 60 fs Qy-Qx IC and demonstrate that it is driven by the interplay among multiple high-frequency modes. Notably, we identify 1510 cm-1 as the leading tuning mode that brings the porphyrin to an optimal geometry for energy surface crossing. By employing coherent wave packet analysis, we highlight a set of short-lived vibrations (1200-1400 cm-1), promoting the IC within ≈60 fs. Furthermore, we identify one coupling mode (1350 cm-1) that is responsible for vibronic mixing within the Q states. Our findings indicate that porphyrin-core functionalization modulates IC effectively, offering new opportunities in photocatalysis and optoelectronics.

Distinguishing Different Stackings in Layered Materials via Luminescence Spectroscopy.

Despite its simple crystal structure, layered boron nitride features a surprisingly complex variety of phonon-assisted luminescence peaks. We present a combined experimental and theoretical study on ultraviolet-light emission in hexagonal and rhombohedral bulk boron nitride crystals. Emission spectra of high-quality samples are measured via cathodoluminescence spectroscopy, displaying characteristic differences between the two polytypes. These differences are explained using a fully first-principles computational technique that takes into account radiative emission from "indirect," finite-momentum excitons via coupling to finite-momentum phonons. We show that the differences in peak positions, number of peaks, and relative intensities can be qualitatively and quantitatively explained, once a full integration over all relevant momenta of excitons and phonons is performed.

Biallelic variants in CEP164 cause a motile ciliopathy-like syndrome.

Ciliopathies may be classed as primary or motile depending on the underlying ciliary defect and are usually considered distinct clinical entities. Primary ciliopathies are associated with multisystem syndromes typically affecting the brain, kidney, and eye, as well as other organ systems such as the liver, skeleton, auditory system, and metabolism. Motile ciliopathies are a heterogenous group of disorders with defects in specialised motile ciliated tissues found within the lung, brain, and reproductive system, and are associated with primary ciliary dyskinesia, bronchiectasis, infertility and rarely hydrocephalus. Primary and motile cilia share defined core ultra-structures with an overlapping proteome, and human disease phenotypes can reflect both primary and motile ciliopathies. CEP164 encodes a centrosomal distal appendage protein vital for primary ciliogenesis. Human CEP164 mutations are typically described in patients with nephronophthisis-related primary ciliopathies but have also been implicated in motile ciliary dysfunction. Here we describe a patient with an atypical motile ciliopathy phenotype and biallelic CEP164 variants. This work provides further evidence that CEP164 mutations can contribute to both primary and motile ciliopathy syndromes, supporting their functional and clinical overlap, and informs the investigation and management of CEP164 ciliopathy patients.

Anomalous non-equilibrium response in black phosphorus to sub-gap mid-infrared excitation.

The competition between the electron-hole Coulomb attraction and the 3D dielectric screening dictates the optical properties of layered semiconductors. In low-dimensional materials, the equilibrium dielectric environment can be significantly altered by the ultrafast excitation of photo-carriers, leading to renormalized band gap and exciton binding energies. Recently, black phosphorus emerged as a 2D material with strongly layer-dependent electronic properties. Here, we resolve the response of bulk black phosphorus to mid-infrared pulses tuned across the band gap. We find that, while above-gap excitation leads to a broadband light-induced transparency, sub-gap pulses drive an anomalous response, peaked at the single-layer exciton resonance. With the support of DFT calculations, we tentatively ascribe this experimental evidence to a non-adiabatic modification of the screening environment. Our work heralds the non-adiabatic optical manipulation of the electronic properties of 2D materials, which is of great relevance for the engineering of versatile van der Waals materials.

Gap Opening in Double-Sided Highly Hydrogenated Free-Standing Graphene.

Conversion of free-standing graphene into pure graphane─where each C atom is sp3 bound to a hydrogen atom─has not been achieved so far, in spite of numerous experimental attempts. Here, we obtain an unprecedented level of hydrogenation (≈90% of sp3 bonds) by exposing fully free-standing nanoporous samples─constituted by a single to a few veils of smoothly rippled graphene─to atomic hydrogen in ultrahigh vacuum. Such a controlled hydrogenation of high-quality and high-specific-area samples converts the original conductive graphene into a wide gap semiconductor, with the valence band maximum (VBM) ∼ 3.5 eV below the Fermi level, as monitored by photoemission spectromicroscopy and confirmed by theoretical predictions. In fact, the calculated band structure unequivocally identifies the achievement of a stable, double-sided fully hydrogenated configuration, with gap opening and no trace of π states, in excellent agreement with the experimental results.

A discarded synonymous variant in NPHP3 explains nephronophthisis and congenital hepatic fibrosis in several families.

Half of patients with a ciliopathy syndrome remain unsolved after initial analysis of whole exome sequencing (WES) data, highlighting the need for improved variant filtering and annotation. By candidate gene curation of WES data, combined with homozygosity mapping, we detected a homozygous predicted synonymous allele in NPHP3 in two children with hepatorenal fibrocystic disease from a consanguineous family. Analyses on patient-derived RNA shows activation of a cryptic mid-exon splice donor leading to frameshift. Remarkably, the same rare variant was detected in four additional families with hepatorenal disease from UK, US, and Saudi patient cohorts and in addition, another synonymous NPHP3 variant was identified in an unsolved case from the Genomics England 100,000 Genomes data set. We conclude that synonymous NPHP3 variants, not reported before and discarded by pathogenicity pipelines, solved several families with a ciliopathy syndrome. These findings prompt careful reassessment of synonymous variants, especially if they are rare and located in candidate genes.

Genetic compensation for cilia defects in cep290 mutants by upregulation of cilia-associated small GTPases.

Mutations in CEP290 (also known as NPHP6), a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish, the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes, whereas deficiencies in a CRISPR/Cas9 genetic mutant were restricted to photoreceptor defects. Here, we show that milder phenotypes in genetic mutants were associated with the upregulation of genes encoding the cilia-associated small GTPases arl3, arl13b and unc119b. Upregulation of UNC119b was also observed in urine-derived renal epithelial cells from human Joubert syndrome CEP290 patients. Ectopic expression of arl3, arl13b and unc119b in cep290 morphant zebrafish embryos rescued Kupffer's vesicle cilia and partially rescued photoreceptor outer segment defects. The results suggest that genetic compensation by upregulation of genes involved in a common subcellular process, lipidated protein trafficking to cilia, may be a conserved mechanism contributing to genotype-phenotype variations observed in CEP290 deficiencies. This article has an associated First Person interview with the first author of the paper.

Gene and epigenetic editing in the treatment of primary ciliopathies.

Primary ciliopathies are inherited human disorders that arise from mutations in ciliary genes. They represent a spectrum of severe, incurable phenotypes, differentially involving several organs, including the kidney and the eye. The development of gene-based therapies is opening up new avenues for the treatment of ciliopathies. Particularly attractive is the possibility of correcting in situ the causative genetic mutation, or pathological epigenetic changes, through the use of gene editing tools. Due to their versatility and efficacy, CRISPR/Cas-based systems represent the most promising gene editing toolkit for clinical applications. However, delivery and specificity issues have so far held back the translatability of CRISPR/Cas-based therapies into clinical practice, especially where systemic administration is required. The eye, with its characteristics of high accessibility and compartmentalization, represents an ideal target for in situ gene correction. Indeed, studies for the evaluation of a CRISPR/Cas-based therapy for in vivo gene correction to treat a retinal ciliopathy have reached the clinical stage. Further technological advances may be required for the development of in vivo CRISPR-based treatments for the kidney. We discuss here the possibilities and the challenges associated to the implementation of CRISPR/Cas-based therapies for the treatment of primary ciliopathies with renal and retinal phenotypes.

Evidence of ideal excitonic insulator in bulk MoS2 under pressure.

Spontaneous condensation of excitons is a long-sought phenomenon analogous to the condensation of Cooper pairs in a superconductor. It is expected to occur in a semiconductor at thermodynamic equilibrium if the binding energy of the excitons-electron (e) and hole (h) pairs interacting by Coulomb force-overcomes the band gap, giving rise to a new phase: the "excitonic insulator" (EI). Transition metal dichalcogenides are excellent candidates for the EI realization because of reduced Coulomb screening, and indeed a structural phase transition was observed in few-layer systems. However, previous work could not disentangle to which extent the origin of the transition was in the formation of bound excitons or in the softening of a phonon. Here we focus on bulk [Formula: see text] and demonstrate theoretically that at high pressure it is prone to the condensation of genuine excitons of finite momentum, whereas the phonon dispersion remains regular. Starting from first-principles many-body perturbation theory, we also predict that the self-consistent electronic charge density of the EI sustains an out-of-plane permanent electric dipole moment with an antiferroelectric texture in the layer plane: At the onset of the EI phase, those optical phonons that share the exciton momentum provide a unique Raman fingerprint for the EI formation. Finally, we identify such fingerprint in a Raman feature that was previously observed experimentally, thus providing direct spectroscopic confirmation of an ideal excitonic insulator phase in bulk [Formula: see text] above 30 GPa.

Update of genetic variants in CEP120 and CC2D2A-With an emphasis on genotype-phenotype correlations, tissue specific transcripts and exploring mutation specific exon skipping therapies.

BACKGROUND: Mutations in ciliary genes cause a spectrum of both overlapping and distinct clinical syndromes (ciliopathies). CEP120 and CC2D2A are paradigmatic examples for this genetic heterogeneity and pleiotropy as mutations in both cause Joubert syndrome but are also associated with skeletal ciliopathies and Meckel syndrome, respectively. The molecular basis for this phenotypical variability is not understood but basal exon skipping likely contributes to tolerance for deleterious mutations via tissue-specific preservation of the amount of expressed functional protein. METHODS: We systematically reviewed and annotated genetic variants and clinical presentations reported in CEP120- and CC2D2A-associated disease and we combined in silico and ex vivo approaches to study tissue-specific transcripts and identify molecular targets for exon skipping. RESULTS: We confirmed more severe clinical presentations associated with truncating CC2D2A mutations. We identified and confirmed basal exon skipping in the kidney, with possible relevance for organ-specific disease manifestations. Finally, we proposed a multimodal approach to classify exons amenable to exon skipping. By mapping reported variants, 14 truncating mutations in 7 CC2D2A exons were identified as potentially rescuable by targeted exon skipping, an approach that is already in clinical use for other inherited human diseases. CONCLUSION: Genotype-phenotype correlations for CC2D2A support the deleteriousness of null alleles and CC2D2A, but not CEP120, offers potential for therapeutic exon skipping approaches.

Cell preservation methods and its application to studying rare disease.

The ability to preserve and transport human cells in a stable medium over long distances is critical to collaborative efforts and the advancement of knowledge in the study of human disease. This is particularly important in the study of rare diseases. Recently, advancements in the understanding of renal ciliopathies has been achieved via the use of patient urine-derived cells (UDCs). However, the traditional method of cryopreservation, although considered as the gold standard, can result in decreased sample viability of many cell types, including UDCs. Delays in transportation can have devastating effects upon the viability of samples, and may even result in complete destruction of cells following evaporation of dry ice or liquid nitrogen, leaving samples in cryoprotective agents, which are cytotoxic at room temperature. The loss of any patient sample in this manner is detrimental to research, however it is even more so when samples are from patients with a rare disease. In order to overcome the associated limitations of traditional practices, new methods of preservation and shipment, including cell encapsulation within hydrogels, and transport in specialised devices are continually being investigated. Here we summarise and compare traditional methods with emerging novel alternatives for the preservation and shipment of cells, and consider the effectiveness of such methods for use with UDCs to further enable the study and understanding of kidney diseases.

Intermolecular conical intersections in molecular aggregates.

Conical intersections (CoIns) of multidimensional potential energy surfaces are ubiquitous in nature and control pathways and yields of many photo-initiated intramolecular processes. Such topologies can be potentially involved in the energy transport in aggregated molecules or polymers but are yet to be uncovered. Here, using ultrafast two-dimensional electronic spectroscopy (2DES), we reveal the existence of intermolecular CoIns in molecular aggregates relevant for photovoltaics. Ultrafast, sub-10-fs 2DES tracks the coherent motion of a vibrational wave packet on an optically bright state and its abrupt transition into a dark state via a CoIn after only 40 fs. Non-adiabatic dynamics simulations identify an intermolecular CoIn as the source of these unusual dynamics. Our results indicate that intermolecular CoIns may effectively steer energy pathways in functional nanostructures for optoelectronics.

Use of patient derived urine renal epithelial cells to confirm pathogenicity of PKHD1 alleles.

BACKGROUND: PKHD1 is the main genetic cause of autosomal recessive polycystic kidney disease (ARPKD), a hereditary hepato-renal fibrocystic disorder which is the most important cause of end-stage renal disease during early childhood. ARPKD can also present in adulthood with milder phenotypes. In this study, we describe a 24-year-old woman with atypical polycystic kidney, no family history of renal disease and no obvious extra-renal manifestations who was referred for genetic investigation. METHODS: We used a combination of next generation sequencing, Sanger sequencing and RNA and microscopy studies performed on urine-derived renal epithelial cells (URECs) to provide a genetic diagnosis of ARPKD. RESULTS: A next generation sequencing panel of cystic ciliopathy genes allowed the identification of two heterozygous sequence changes in PKHD1 (c.6900C > T; p.(Asn2300=) and c.7964A > C; p.(His2655Pro)). The pathogenicity of the synonymous PKHD1 variant is not clear and requires RNA studies, which cannot be carried out efficiently on RNA extracted from proband blood, due to the low expression levels of PKHD1 in lymphocytes. Using URECs as a source of kidney-specific RNA, we show that PKHD1 is alternatively spliced around exon 43, both in control and proband URECs. The variant p.(Asn2300=) shifts the expression ratio in favour of a shorter, out-of-frame transcript. To further study the phenotypic consequence of these variants, we investigated the ciliary phenotype of patient URECs, which were abnormally elongated and presented multiple blebs along the axoneme. CONCLUSIONS: We confirm the power of URECs as a tool for functional studies on candidate variants in inherited renal disease, especially when the expression of the gene of interest is restricted to the kidney and we describe, for the first time, ciliary abnormalities in ARPKD patient cells.

Vibrational signature of the graphene nanoribbon edge structure from high-resolution electron energy-loss spectroscopy.

Bottom-up approaches exploiting on-surface synthesis reactions allow atomic-scale precision in the fabrication of graphene nanoribbons (GNRs); this is essential for their technological applications since their unique electronic and optical properties are largely controlled by the specific edge structure. By means of a combined experimental-theoretical investigation of some prototype GNRs, we show here that high-resolution electron energy-loss spectroscopy (HREELS) can be successfully employed to fingerprint the details of the GNR edge structure. In particular, we demonstrate how the features of HREEL vibrational spectra - mainly dictated by edge CH out-of-plane modes - are unambiguously related to the GNR edge structure. Moreover, we single out those modes which are localized at the GNR termini and show how their relative intensity can be related to the average GNR length.

Clinical and genetic characteristics of autosomal recessive polycystic kidney disease in Oman.

BACKGROUND: There is a high prevalence of rare genetic disorders in the Middle East, and their study provides unique clinical and genetic insights. Autosomal recessive polycystic kidney disease (ARPKD) is one of the leading causes of kidney and liver-associated morbidity and mortality in Oman. We describe the clinical and genetic profile of cohort of ARPKD patients. METHODS: We studied patients with a clinical diagnosis of ARPKD (n = 40) and their relatives (parents (n = 24) and unaffected siblings (n = 10)) from 32 apparently unrelated families, who were referred to the National Genetic Centre in Oman between January 2015 and December 2018. Genetic analysis of PKHD1 if not previously known was performed using targeted exon PCR of known disease alleles and Sanger sequencing. RESULTS: A clinical diagnosis of ARPKD was made prenatally in 8 patients, 21 were diagnosed during infancy (0-1 year), 9 during early childhood (2-8 years) and 2 at later ages (9-13 years). Clinical phenotypes included polycystic kidneys, hypertension, hepatic fibrosis and splenomegaly. Twenty-four patients had documented chronic kidney disease (median age 3 years). Twenty-four out of the 32 families had a family history suggesting an autosomal recessive pattern of inherited kidney disease, and there was known consanguinity in 21 families (66%). A molecular genetic diagnosis with biallelic PKHD1 mutations was known in 18 patients and newly identified in 20 other patients, totalling 38 patients from 30 different families. Two unrelated patients remained genetically unsolved. The different PKHD1 missense pathogenic variants were: c.107C > T, p.(Thr36Met); c.406A > G, p.(Thr136Ala); c.4870C > T, p.(Arg1624Trp) and c.9370C > T, p.(His3124Tyr) located in exons 3, 6, 32 and 58, respectively. The c.406A > G, p.(Thr136Ala) missense mutation was detected homozygously in one family and heterozygously with a c.107C > T, p.(Thr36Met) allele in 5 other families. Overall, the most commonly detected pathogenic allele was c.107C > T; (Thr36Met), which was seen in 24 families. CONCLUSIONS: Molecular genetic screening of PKHD1 in clinically suspected ARPKD cases produced a high diagnostic rate. The limited number of PKHD1 missense variants identified in ARPKD cases suggests these may be common founder alleles in the Omani population. Cost effective targeted PCR analysis of these specific alleles can be a useful diagnostic tool for future cases of suspected ARPKD in Oman.

Disease Modeling To Understand the Pathomechanisms of Human Genetic Kidney Disorders.

The class of human genetic kidney diseases is extremely broad and heterogeneous. Accordingly, the range of associated disease phenotypes is highly variable. Many children and adults affected by inherited kidney disease will progress to ESKD at some point in life. Extensive research has been performed on various different disease models to investigate the underlying causes of genetic kidney disease and to identify disease mechanisms that are amenable to therapy. We review some of the research highlights that, by modeling inherited kidney disease, contributed to a better understanding of the underlying pathomechanisms, leading to the identification of novel genetic causes, new therapeutic targets, and to the development of new treatments. We also discuss how the implementation of more efficient genome-editing techniques and tissue-culture methods for kidney research is providing us with personalized models for a precision-medicine approach that takes into account the specificities of the patient and the underlying disease. We focus on the most common model systems used in kidney research and discuss how, according to their specific features, they can differentially contribute to biomedical research. Unfortunately, no definitive treatment exists for most inherited kidney disorders, warranting further exploitation of the existing disease models, as well as the implementation of novel, complex, human patient-specific models to deliver research breakthroughs.

A monolayer transition-metal dichalcogenide as a topological excitonic insulator.

Monolayer transition-metal dichalcogenides in the T' phase could enable the realization of the quantum spin Hall effect1 at room temperature, because they exhibit a prominent spin-orbit gap between inverted bands in the bulk2,3. Here we show that the binding energy of electron-hole pairs excited through this gap is larger than the gap itself in the paradigmatic case of monolayer T' MoS2, which we investigate from first principles using many-body perturbation theory4. This paradoxical result hints at the instability of the T' phase in the presence of spontaneous generation of excitons, and we predict that it will give rise to a reconstructed 'excitonic insulator' ground state5-7. Importantly, we show that in this monolayer system, topological and excitonic order cooperatively enhance the bulk gap by breaking the crystal inversion symmetry, in contrast to the case of bilayers8-16 where the frustration between the two orders is relieved by breaking time reversal symmetry13,15,16. The excitonic topological insulator is distinct from the bare topological phase because it lifts the band spin degeneracy, which results in circular dichroism. A moderate biaxial strain applied to the system leads to two additional excitonic phases, different in their topological character but both ferroelectric17,18 as an effect of electron-electron interaction.

Mouse genetics reveals Barttin as a genetic modifier of Joubert syndrome.

Genetic and phenotypic heterogeneity and the lack of sufficiently large patient cohorts pose a significant challenge to understanding genetic associations in rare disease. Here we identify Bsnd (alias Barttin) as a genetic modifier of cystic kidney disease in Joubert syndrome, using a Cep290-deficient mouse model to recapitulate the phenotypic variability observed in patients by mixing genetic backgrounds in a controlled manner and performing genome-wide analysis of these mice. Experimental down-regulation of Bsnd in the parental mouse strain phenocopied the severe cystic kidney phenotype. A common polymorphism within human BSND significantly associates with kidney disease severity in a patient cohort with CEP290 mutations. The striking phenotypic modifications we describe are a timely reminder of the value of mouse models and highlight the significant contribution of genetic background. Furthermore, if appropriately managed, this can be exploited as a powerful tool to elucidate mechanisms underlying human disease heterogeneity.

A CEP104-CSPP1 Complex Is Required for Formation of Primary Cilia Competent in Hedgehog Signaling.

CEP104 is an evolutionarily conserved centrosomal and ciliary tip protein. CEP104 loss-of-function mutations are reported in patients with Joubert syndrome, but their function in the etiology of ciliopathies is poorly understood. Here, we show that cep104 silencing in zebrafish causes cilia-related manifestations: shortened cilia in Kupffer's vesicle, heart laterality, and cranial nerve development defects. We show that another Joubert syndrome-associated cilia tip protein, CSPP1, interacts with CEP104 at microtubules for the regulation of axoneme length. We demonstrate in human telomerase reverse transcriptase-immortalized retinal pigmented epithelium (hTERT-RPE1) cells that ciliary translocation of Smoothened in response to Hedgehog pathway stimulation is both CEP104 and CSPP1 dependent. However, CEP104 is not required for the ciliary recruitment of CSPP1, indicating that an intra-ciliary CEP104-CSPP1 complex controls axoneme length and Hedgehog signaling competence. Our in vivo and in vitro analyses of CEP104 define its interaction with CSPP1 as a requirement for the formation of Hedgehog signaling-competent cilia, defects that underlie Joubert syndrome.

Targeted exon skipping rescues ciliary protein composition defects in Joubert syndrome patient fibroblasts.

Joubert syndrome (JBTS) is an incurable multisystem ciliopathy syndrome. The most commonly mutated gene in JBTS patients with a cerebello-retinal-renal phenotype is CEP290 (alias JBTS5). The encoded CEP290 protein localises to the proximal end of the primary cilium, in the transition zone, where it controls ciliary protein composition and signalling. We examined primary cilium structure and composition in fibroblast cells derived from homozygous and compound heterozygous JBTS5 patients with nonsense mutations in CEP290 and show that elongation of cilia, impaired ciliogenesis and ciliary composition defects are typical features in JBTS5 cells. Targeted skipping of the mutated exon c.5668 G > T using antisense oligonucleotide (ASO) therapy leads to restoration of CEP290 protein expression and functions at the transition zone in homozygous and compound heterozygous JBTS5 cells, allowing a rescue of both cilia morphology and ciliary composition. This study, by demonstrating that targeted exon skipping is able to rescue ciliary protein composition defects, provides functional evidence for the efficacy of this approach in the treatment of JBTS.