ALBERT

Description: The enigmatic monocot family Triuridaceae provides a potentially useful model system for studying the effects of an ancient loss of photosynthesis on the plant plastid genome, as all of its members are mycoheterotrophic and achlorophyllous. However, few studies have placed the family in a comparative context, and its phylogenetic placement is only partly resolved. It was also unclear whether any taxa in this family have retained a plastid genome. Here, we used genome survey sequencing to retrieve plastid genome data for Sciaphila densiflora (Triuridaceae) and ten autotrophic relatives in the orders Dioscoreales and Pandanales. We recovered a highly reduced plastome for Sciaphila that is nearly colinear with Carludovica palmata , a photosynthetic relative that belongs to its sister group in Pandanales, Cyclanthaceae–Pandanaceae. This phylogenetic placement is well supported and robust to a broad range of analytical assumptions in maximum-likelihood inference, and is congruent with recent findings based on nuclear and mitochondrial evidence. The 28 genes retained in the S. densiflora plastid genome are involved in translation and other nonphotosynthetic functions, and we demonstrate that nearly all of the 18 protein-coding genes are under strong purifying selection. Our study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.

Description: Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis -spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.

Description: We correct a mistake in the proof of Theorem 1 of the paper in the title.

Description: De novo disruptions of the neural transcription factor FOXP1 are a recently discovered, rare cause of sporadic intellectual disability (ID). We report three new cases of FOXP1 -related disorder identified through clinical whole-exome sequencing. Detailed phenotypic assessment confirmed that global developmental delay, autistic features, speech/language deficits, hypotonia and mild dysmorphic features are core features of the disorder. We expand the phenotypic spectrum to include sensory integration disorder and hypertelorism. Notably, the etiological variants in these cases include two missense variants within the DNA-binding domain of FOXP1. Only one such variant has been reported previously. The third patient carries a stop-gain variant. We performed functional characterization of the three missense variants alongside our stop-gain and two previously described truncating/frameshift variants. All variants severely disrupted multiple aspects of protein function. Strikingly, the missense variants had similarly severe effects on protein function as the truncating/frameshift variants. Our findings indicate that a loss of transcriptional repression activity of FOXP1 underlies the neurodevelopmental phenotype in FOXP1-related disorder. Interestingly, the three novel variants retained the ability to interact with wild-type FOXP1, suggesting these variants could exert a dominant-negative effect by interfering with the normal FOXP1 protein. These variants also retained the ability to interact with FOXP2, a paralogous transcription factor disrupted in rare cases of speech and language disorder. Thus, speech/language deficits in these individuals might be worsened through deleterious effects on FOXP2 function. Our findings highlight that de novo FOXP1 variants are a cause of sporadic ID and emphasize the importance of this transcription factor in neurodevelopment.

Description: CRISPR-Cas is an RNA-guided adaptive immune system that protects bacteria and archaea from invading nucleic acids. Type III systems (Cmr, Csm) have been shown to cleave RNA targets in vitro and some are capable of transcription-dependent DNA targeting. The crenarchaeon Sulfolobus solfataricus has two divergent subtypes of the type III system (Sso-IIID and a Cmr7-containing variant of Sso-IIIB). Here, we report that both the Sso-IIID and Sso-IIIB complexes cleave cognate RNA targets with a ruler mechanism and 6 or 12 nt spacing that relates to the organization of the Cas7 backbone. This backbone-mediated cleavage activity thus appears universal for the type III systems. The Sso-IIIB complex is also known to possess a distinct ‘UA’ cleavage mode. The predominant activity observed in vitro depends on the relative molar concentration of protein and target RNA. The Sso-IIID complex can cleave plasmid DNA targets in vitro, generating linear DNA products with an activity that is dependent on both the cyclase and HD nuclease domains of the Cas10 subunit, suggesting a role for both nuclease active sites in the degradation of double-stranded DNA targets.

Description: Biomass energy is growing worldwide as generators continue their search for sustainable energy sources. This project focuses on the storage of biomass fuels, investigating degradation. Four different fuels were stored in air-tight buckets for 9 months to promote artificial degradation and provide an initial benchmark in a long-term project investigating the impact of different storage scenarios on a range of fuels. At regular intervals, samples were taken out of buckets for analysis including stereo zoom microscopy and thermogravimetric analysis. Fungal analysis was carried out on two degraded fuels.

Description: We use continuous GPS measurements from 31 stations in southern Mexico to model coseismic slip and post-seismic deformation from the 2012 March 20 M w  = 7.5 Ometepec earthquake, the first large thrust earthquake to occur below central Mexico during the modern GPS era. Coseismic offsets ranging from ~280 mm near the epicentre to 5 mm or less at sites far from the epicentre are fit best by a rupture focused between ~15 and 35 km depth, consistent with an independent seismological estimate. The corresponding geodetic moment of 1.4 10 20 N·m is within 10 per cent of two independent seismic estimates. Transient post-seismic motion recorded by GPS sites as far as 300 km from the rupture has a different horizontal deformation gradient and opposite sense of vertical motion than do the coseismic offsets. A forward model of viscoelastic relaxation as a result of our new coseismic slip solution incorrectly predicts uplift in areas where post-seismic subsidence was recorded and indicates that viscoelastic deformation was no more than a few per cent of the measured post-seismic deformation. The deformation within 6 months of the earthquake was thus strongly dominated by fault afterslip. The post-seismic GPS time-series are well fit as logarithmically decaying fault afterslip on an area of the subduction interface up to 10 times larger than the earthquake rupture zone, extending as far as 220 km inland. Afterslip had a cumulative geodetic moment of 2.0 10 20 N·m, ~40 per cent larger than the Ometepec earthquake. Tests for the shallow and deep limits for the afterslip require that it included much of the earthquake rupture zone as well as regions of the subduction interface where slow slip events and non-volcanic tremor have been recorded and areas even farther downdip on the flat interface. Widespread afterslip below much of central Mexico suggests that most of the nearly flat subduction interface in this region is conditionally stable and thus contributes measurable transient deformation to large areas of Mexico south of and in the volcanic belt.

Description: The plant hormone auxin is a conserved regulator of development which has been implicated in the generation of morphological novelty. PIN-FORMED1 (PIN) auxin efflux carriers are central to auxin function by regulating its distribution. PIN family members have divergent structures and cellular localizations, but the origin and evolutionary significance of this variation is unresolved. To characterize PIN family evolution, we have undertaken phylogenetic and structural analyses with a massive increase in taxon sampling over previous studies. Our phylogeny shows that following the divergence of the bryophyte and lycophyte lineages, two deep duplication events gave rise to three distinct lineages of PIN proteins in euphyllophytes. Subsequent independent radiations within each of these lineages were taxonomically asymmetric, giving rise to at least 21 clades of PIN proteins, of which 15 are revealed here for the first time. Although most PIN protein clades share a conserved canonical structure with a modular central loop domain, a small number of noncanonical clades dispersed across the phylogeny have highly divergent protein structure. We propose that PIN proteins underwent sub- and neofunctionalization with substantial modification to protein structure throughout plant evolution. Our results have important implications for plant evolution as they suggest that structurally divergent PIN proteins that arose in paralogous radiations contributed to the convergent evolution of organ systems in different land plant lineages.

Description: We model measurements from 19 continuous GPS stations to determine the location and magnitude of a slow slip event (SSE) below southern Mexico that began in late 2011 and remained active up to the 2012 March 20 M w  = 7.4 Ometepec earthquake. Modelling of the space–time evolution of the SSE indicates that it initiated in 2011 November, migrated westward ~2.6 km per day along the subduction interface, and reached the eventual earthquake source region ~1 month before the 2012 March 20 earthquake occurred, in the waning stage of the SSE. The maximum slip for the SSE, ~100 mm, occurred ~100 km east of the earthquake rupture zone, in contrast to slip of 10–20 mm proximal to the Ometepec rupture zone. The SSE was focused downdip from the seismogenic zone everywhere along its ~300-km-wide slip region and had a cumulative moment release of 3.0 10 19 N•m ( M w  = 6.9), similar to SSEs in 2004 and 2006 along this same area of the subduction interface. We calculate Coulomb stress changes as a result of slip during the SSE and find small but positive stress changes for the source region of the Ometepec earthquake. Our results are consistent with the hypothesis that the SSE triggered the Ometepec earthquake, although they are insufficient to demonstrate causality.

Description: CRISPR-Cas is an adaptive prokaryotic immune system, providing protection against viruses and other mobile genetic elements. In type I and type III CRISPR-Cas systems, CRISPR RNA (crRNA) is generated by cleavage of a primary transcript by the Cas6 endonuclease and loaded into multisubunit surveillance/effector complexes, allowing homology-directed detection and cleavage of invading elements. Highly studied CRISPR-Cas systems such as those in Escherichia coli and Pseudomonas aeruginosa have a single Cas6 enzyme that is an integral subunit of the surveillance complex. By contrast, Sulfolobus solfataricus has a complex CRISPR-Cas system with three types of surveillance complexes (Cascade/type I-A, CSM/type III-A and CMR/type III-B), five Cas6 paralogues and two different CRISPR-repeat families (AB and CD). Here, we investigate the kinetic properties of two different Cas6 paralogues from S. solfataricus . The Cas6-1 subtype is specific for CD-family CRISPR repeats, generating crRNA by multiple turnover catalysis whilst Cas6-3 has a broader specificity and also processes a non-coding RNA with a CRISPR repeat-related sequence. Deep sequencing of crRNA in surveillance complexes reveals a biased distribution of spacers derived from AB and CD loci, suggesting functional coupling between Cas6 paralogues and their downstream effector complexes.