Genome architecture and stability in the Saccharomyces cerevisiae knockout collection

Despite major progress in defining the functional roles of genes, a complete understanding of their influences is far from being realized, even in relatively simple organisms. A major milestone in this direction arose via the completion of the yeast Saccharomyces cerevisiae gene-knockout collection (YKOC), which has enabled high-throughput reverse genetics, phenotypic screenings and analyses of synthetic-genetic interactions1-3. Ensuing experimental work has also highlighted some inconsistencies and mistakes in the YKOC, or genome instability events that rebalance the effects of specific knockouts4-6, but a complete overview of these is lacking. The identification and analysis of genes that are required for maintaining genomic stability have traditionally relied on reporter assays and on the study of deletions of individual genes, but whole-genome-sequencing technologies now enable-in principle-the direct observation of genome instability globally and at scale. To exploit this opportunity, we sequenced the whole genomes of nearly all of the 4,732 strains comprising the homozygous diploid YKOC. Here, by extracting information on copy-number variation of tandem and interspersed repetitive DNA elements, we describe-for almost every single non-essential gene-the genomic alterations that are induced by its loss. Analysis of this dataset reveals genes that affect the maintenance of various genomic elements, highlights cross-talks between nuclear and mitochondrial genome stability, and shows how strains have genetically adapted to life in the absence of individual non-essential genes.

Visual acuity and contrast sensitivity are two important factors affecting vision-related quality of life in advanced age-related macular degeneration

PURPOSE

Vision loss from age-related macular degeneration (AMD) has a profound effect on vision-related quality of life (VRQoL). The pupose of this study is to identify clinical factors associated with VRQoL using the Rasch- calibrated NEI VFQ-25 scales in bilateral advanced AMD patients.

METHODS

We retrospectively reviewed 47 patients (mean age 83.2 years) with bilateral advanced AMD. Clinical assessment included age, gender, type of AMD, high contrast visual acuity (VA), history of medical conditions, contrast sensitivity (CS), central visual field loss, report of Charles Bonnet Syndrome, current treatment for AMD and Rasch-calibrated NEI VFQ-25 visual function and socioemotional function scales. The NEI VFQ visual function scale includes items of general vision, peripheral vision, distance vision and near vision-related activity while the socioemotional function scale includes items of vision related-social functioning, role difficulties, dependency, and mental health. Multiple regression analysis (structural regression model) was performed using fixed item parameters obtained from the one-parameter item response theory model.

RESULTS

Multivariate analysis showed that high contrast VA and CS were two factors influencing VRQoL visual function scale (β = -0.25, 95% CI-0.37 to -0.12, p<0.001 and β = 0.35, 95% CI 0.25 to 0.46, p<0.001) and socioemontional functioning scale (β = -0.2, 95% CI -0.37 to -0.03, p = 0.023, and β = 0.3, 95% CI 0.18 to 0.43, p = 0.001). Central visual field loss was not assoicated with either VRQoL visual or socioemontional functioning scale (β = -0.08, 95% CI-0.28 to 0.12,p = 0.44 and β = -0.09, 95% CI -0.03 to 0.16, p = 0.50, respectively).

CONCLUSION

In patients with vision impairment secondary to bilateral advanced AMD, high contrast VA and CS are two important factors affecting VRQoL.

Adding access to a video magnifier to standard vision rehabilitation: initial results on reading performance and well-being from a prospective, randomized study

PURPOSE

Both optical and electronic magnification are available to patients with low vision. Electronic video magnifiers are more expensive than optical magnifiers, but they offer additional benefits, including variable magnification and contrast. This study aimed to evaluate the effect of access to a video magnifier (VM) added to standard comprehensive vision rehabilitation (VR).

METHODS

In this prospective study, 37 subjects with central field loss were randomized to receive standard VR (VR group, 18 subjects) or standard VR plus VM (VM group, 19 subjects). Subjects read the International Reading Speed Texts (IReST), a bank check, and a phone number at enrollment, at 1 month, and after occupational therapy (OT) as indicated to address patient goals. The Impact of Vision Impairment (IVI) questionnaire, a version of the Activity Inventory (AI), and the Depression Anxiety and Stress Scale (DASS) were administered at enrollment, 1 month, after OT, 1 month later, and 1 year after enrollment. Assessments at enrollment and 1 month later were evaluated.

RESULTS

At 1 month, the VM group displayed significant improvement in reading continuous print as measured by the IReST (P = 0.01) but did not differ on IVI, AI, or DASS. From enrollment to 1 month all subjects improved in their ability to spot read (phone number and check; P < 0.01 for both). The VM group improved in their ability to find and read a number in a phone book more than the VR group at 1 month after initial consultation (P = 0.02). All reported better well-being (P = 0.02).

CONCLUSIONS

All subjects reported better well-being on the IVI. The VM group read faster and was better at two spot reading tasks but did not differ from the VR group in other outcome measures.

High-throughput assessment of transgene copy number in sugarcane using real-time quantitative PCR

Accurate and timely detection of transgene copy number in sugarcane is currently hampered by the requirement to use Southern blotting, needing relatively large amounts of genomic DNA and, therefore, the continued growth and maintenance of bulky plants in containment glasshouses. In addition, the sugarcane genome is both polyploid and aneuploid, complicating the identification of appropriate genes for use as references in the development of a high-throughput method. Using bioinformatic techniques followed by in vitro testing, two genes that appear to occur once per base genome of sugarcane were identified. Using these genes as reference genes, a high-throughput assay employing RT-qPCR was developed and tested using a group of sugarcane plants that contained unknown numbers of copies of the nptII gene encoding kanamycin resistance. Using this assay, transgene copy numbers from 3 to more than 50 were identified. In comparison, Southern blotting accurately identified the number of transgene copies for one line and by inference for another, but was not able to provide an accurate estimation for transgenic lines containing numerous copies of the nptII gene. Using the reference genes identified in this study, a high-throughput assay for the determination of transgene copy number was developed and tested for sugarcane. This method requires much less input DNA, can be performed much earlier in the production of transgenic sugarcane plants and allows much more efficient assessment of numerous potentially transgenic lines than Southern blotting.

Minimal length requirement for proteasomal degradation of ubiquitin-dependent substrates

An erroneous transcriptional process, known as molecular misreading, gives rise to an alternative transcript of the ubiquitin B (UBB) gene. This transcript encodes the protein UBB(+1), which comprises a ubiquitin moiety and a 19-aa C-terminal extension. UBB(+1) is found in affected neurons in neurodegenerative diseases and behaves as an atypical ubiquitin fusion degradation (UFD) proteasome substrate that is poorly degraded and impedes the ubiquitin/proteasome system. Here, we show that the limited length of UBB(+1) is responsible for its inefficient degradation and inhibitory activity. Designed UFD substrates with an equally short 19-aa or a 20-aa C-terminal extension were also poorly degraded and had a general inhibitory activity on the ubiquitin/proteasome system in two unrelated cell lines. Extending the polypeptide to 25 aa sufficed to convert the protein into an efficiently degraded proteasome substrate that lacked inhibitory activity. A similar length dependency was found for degradation of two UFD substrates in Saccharomyces cerevisiae, which suggests that the mechanisms underlying this length constraint are highly conserved. Extending UBB(+1) also converted this protein into an efficient substrate of the proteasome. These observations provide an explanation for the accumulation of UBB(+1) in neurodegenerative disorders and offers new insights into the physical constraints determining proteasomal degradation.

Biogenesis and processing of the amyloid precursor protein in the early secretory pathway

The beta-amyloid peptide is an aggregation-prone peptide that is released from the amyloid precursor protein (APP) after cleavage by the beta- and gamma-secretase. A number of studies have suggested that processing of APP by beta- and gamma-secretase occurs not only at the cell surface and in the endosomal compartments but also in the endoplasmic reticulum (ER) and Golgi complex. Here, we studied the role of the early secretory pathway in processing of APP. For this purpose, APP was in vitro translated in semi-permeabilized cells, which have a functionally intact ER and Golgi complex but lack a functional plasma membrane. We show that the beta-secretase cleavage product C99 is generated in the early secretory pathway. Moreover, nicastrin and presenilin, two components of the gamma-secretase complex, interacted with newly synthesized APP. Administration of the gamma-secretase inhibitor L685,458 caused accumulation of full length APP and C99. Full length APP but not C99 interacted with several protein quality control ER chaperones including the thiol oxidoreductase ERp57. Our in vitro study suggests that newly synthesized APP is subject to amyloidogenic processing during the initial phases of the secretory pathway.

COPI-mediated retrograde transport is required for efficient γ-secretase cleavage of the amyloid precursor protein

Sequential cleavage of the amyloid precursor protein (APP) by beta- and gamma-secretases results in the production of beta-amyloid peptide, which is a key determinant in Alzheimer's disease. Since several putative locations for gamma-secretase cleavage have been identified along the secretory pathway, trafficking of APP may be of importance for beta-amyloid peptide production. Here we have studied the role of retrograde transport in APP processing. We found that APP interacts with the beta subunit of the coatomer protein I (COPI) complex, which is involved in retrograde transport. In line with a role of retrograde trafficking in APP transport, inhibition of COPI-dependent transport altered APP trafficking, decreased APP cell surface expression, and coincided with a profound reduction in gamma-secretase cleavage. These results suggest that COPI-dependent retrograde transport is important for APP processing and influences production of beta-amyloid peptide.