Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells.

Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics.

Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.

High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly.

BACKGROUND: Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative repeat consensuses be derived from unassembled genomes? RESULTS: Here, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplification setups, and (3) specific repeat-centred questions, such as the linked vs. unlinked arrangement of ribosomal genes. In all our use cases, the derived consensuses are robust and representative. To evaluate overall performance, we compare our high-fidelity repeat consensuses to RepeatExplorer2-derived contigs and check, if they represent real transposable elements as found in long reads. Our results demonstrate that it is possible to generate useful, reliable and trustworthy consensuses from short reads by a combination from read cluster and genome assembly methods in an automatable way. CONCLUSION: We anticipate that our workflow opens the way towards more efficient and less manual repeat characterization and annotation, benefitting all genome studies, but especially those of non-model organisms.

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets.

Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.

Preparation of Mitotic Chromosomes with the Dropping Technique.

The quality of chromosome preparation influences all downstream analyses and is therefore crucial. Hence, numerous protocols exist to produce microscopic slides with mitotic chromosomes. Nevertheless, due to the high content of fibers in and around a plant cell, preparation of plant chromosomes is still far from trivial and needs to be fine-tuned for each species and tissue type. Here, we outline the "dropping method," a straightforward and efficient protocol to prepare multiple slides with uniform quality from a single chromosome preparation. In this method, nuclei are extracted and cleaned to produce a nuclei suspension. In a drop-by-drop manner, this suspension is then applied from a certain height onto the slides, causing the nuclei to rupture and the chromosomes to spread. Due to the physical forces that accompany the dropping and spreading process, this method is best suited for species with small- to medium-sized chromosomes.

A kinetic study of the photolysis of sulfamethoxazole with special emphasis on the photoisomer.

The previously not studied photochemical degradation of sulfamethoxazole (SMX) to the isomer of SMX (ISO) was measured via a polychromatic (Xe) and a monochromatic (Hg) light source and accompanied by quantum chemical DFT calculations. In addition to the [Formula: see text] of ISO, tautomer-dependent properties such as the [Formula: see text] were measured and theoretically confirmed by DFT. The kinetics in solutions below and above the [Formula: see text] of SMX were studied for the available and quantifiable products SMX, ISO, 3-amino-5-methylisoxazole (AMI), 2-amino-5-methyloxazole (AMO), and sulfanilic acid (SUA). The quantum yields of the neutral ([Formula: see text]) and anionic [Formula: see text]) forms of SMX ([Formula: see text], [Formula: see text]) and ISO ([Formula: see text] and [Formula: see text]) were found to be wavelength-independent. In a competitive reaction to the formation of ISO from SMX, the degradation product TP271 is formed. Various proposed structures for TP271 described in the literature have been studied quantum mechanically and can be excluded for thermodynamic reasons. In real samples in a northern German surface water in summer 2021 mean concentrations of SMX were found in the range of 120 ng/L. In agreement with the pH-dependent yields, concentrations of ISO were low in the range of 8 ng/L.

Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA.

Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate.

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives.

BACKGROUND: As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes - traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. RESULTS: We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. CONCLUSION: In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa.

Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris).

BACKGROUND AND AIMS: Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. METHODS: Using next- and third-generation sequencing data and genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance and distribution by fluorescent in situ and Southern hybridization. KEY RESULTS: Full-length beetEPRVs range between 7.5 and 10.7 kb in size, are heterogeneous in structure and sequence, and occupy about 0.3 % of the beet genome. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in the vicinity of each other and are associated with heterochromatic, centromeric and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4-7.2 million years ago. CONCLUSIONS: Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing implies possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.

Influence on interradicular bone volume of Invisalign treatment for adult crowding with interproximal enamel reduction: a retrospective three-dimensional cone-beam computed tomography study.

BACKGROUND: The aim of this study was to use three-dimensional datasets to identify associations between treatment for adult crowding, using Invisalign aligner and interproximal enamel reduction (IER), and changes in the volume of interradicular bone. METHODS: A total of 60 cone-beam computed tomography (CBCT) scans from 30 adult patients (28 women, two men; 30 CBCTs pre-treatment, 30 post-treatment) were examined retrospectively in order to measure bone volume three-dimensionally. The patients' average age was 36.03 ± 9.7 years. The interradicular bone volume was measured with OsiriX at four levels in the anterior tooth areas of the maxilla and mandible. Differences in bone between T0 and T1 were analyzed with IBM SPSS 21.0 using the Wilcoxon test for paired samples. RESULTS: Overall, a slight increase in the quantity of bone was found (0.12 ± 0.73 mm). There was a highly significant increase in bone in the mandible (0.40 ± 0.62 mm; P <  0.001), while in the maxilla there was a slight loss of bone, which was highly significant in the apical third (- 0.16 ± 0.77 mm; P = 0.001). CONCLUSIONS: Overall, treatment for adult crowding using an aligner and IER appears to have a positive effect on interradicular bone volume, particularly in patients with severe grades of the condition (periodontally high-risk dentition). This effect is apparently independent of IER. This is extremely important with regard to the treatment outcome, since IER and root proximity have been matters of debate in the literature and teeth should remain firmly embedded in their alveolar sockets.

Influence of Invisalign treatment with interproximal enamel reduction (IER) on bone volume for adult crowding: a retrospective three-dimensional cone beam computed tomography study.

BACKGROUND: The aim of this study was to use three-dimensional datasets to identify associations between treatment for adult crowding using Invisalign and interproximal enamel reduction (IER) and changes in the bone volume. METHODS: A total of 60 digital cone beam computed tomography (CBCT) scans from 30 patients (28 women, two men; 30 CBCTs pretreatment, 30 posttreatment) were examined retrospectively in order to record bone volume three-dimensionally before and after treatment. The patients' average age was 36.03 ± 9.7 years. The data were collected and analyzed using the computer programs Mimics 15.0 and OsiriX. Differences in bone between T0 and T1 were analyzed with IBM SPSS 21.0 using the Wilcoxon test for paired samples. RESULTS: Analysis of the orovestibular bone volume showed highly significant changes (bone change P <0.001) only in the mandible where more expansion of the dental arch was carried out using proclination or protrusion. The bone lamella was thinner buccally and thicker lingually. In general, bone increases in the oral direction were slightly greater than bone losses in the vestibular direction. No significant changes were detected in the maxilla (bone change P = 0.13). Significant vertical bone loss in the bone height was detected in both the maxilla and the mandible. The largest bone loss was observed in the vestibular direction in the mandible, at a high level of significance (P <0.001). CONCLUSIONS: Particularly in the mandible, therapeutic reduction of the vertical and sagittal bone volume shows that caution should be used in the treatment of tertiary crowding with proclination and expansion. The cortical walls appear to represent the limits for orthodontic tooth movement, at least in adult female patients.