Analyses of the 5-prime Ends of Escherichia coli ORFs

Sequence biases at 5-prime ends of coding sequences differ from those of the remainder of ORFs, reflecting differences in function. Internal sequence biases promote translational efficiency by several mechanisms including correlating codon usage and tRNA concentration. However, the early region may also facilitate translational initiation, establishment of the reading frame, and polypeptide processing. Here we examine the beginnings of the ORFs of an Escherichia coli K12 reference genome. The results extend previous observations of A-richness to include an overabundance of the AAA triplet in all reading frames, consistent with the hypothesis that the beginnings of ORFs contribute to initiation site accessibility. Results are also consistent with the idea that the first two amino acids are under selection because they facilitate solvation of the amino-terminus at the end of the ribosomal exit channel. Moreover, serine is highly overrepresented as the second amino acid, possibly because it can facilitate removal of the terminal formylmethionine. Non-AUG initiation codons are known to be less efficient than AUG at directing initiation, presumably because of relatively weak base pairing to the initiator-tRNA. But non-UAG initiation codons are not followed by unusual 3-prime nearest neighbor codons. Moreover, the four NUG initiation codons do not differ in their propensity to frameshift in an assay known to be sensitive to base pair strength. Altogether, these data suggest that the 5-prime ends of ORFs are under selection for several functions, and that initiation codon identity may not critical beyond its role in initiation.

Feline Coronaviruses Identified in Feline Effusions in Suspected Cases of Feline Infectious Peritonitis

Ninety-five effusion samples were collected from cats with suspected feline infectious peritonitis in northern Taiwan; these samples showed a 47.4% (45/95) feline coronavirus (FCoV) positivity rate on immunofluorescence staining and RT-PCR. Young cats (≤24 months old) were found to have a significantly higher risk than cats >24 months old (odds ratio (OR) = 6.19, 95% confidence interval (CI) 2.54–16.00). No significant association was found between the positive rates and sex or breed. The A/G ratio in positive cases was significantly lower than the A/G ratio in negative cases. Genotyping and sequencing of the positive cases revealed 71.9% single infection with type I strains and 28.1% coinfection with types I and II. No single infections with type II strains were noted. The type I sequences had high diversity, while the type II sequences had high internal sequence identity and were more similar to CoVs from other species, such as dogs, pigs, and various small mammals. This study demonstrates the latest analysis of FCoV infection cases in northern Taiwan.

Analysis of the validity and accuracy of the scale of the creative leadership qualities of school administrators

The purpose of this research is to check the validity and accuracy of “Scale of The Creative Leadership Qualities of School Administrators” by Uchar and Saghlam (2019) in case of Azerbaijan. In total, 613 teachers have completed this survey. The “Scale” has been supported by the values (scores) acquired from the linguistic equivalence and correlation between Azerbaijani and Turkish versions. The research has concluded that there was no necessity to reevaluate the describing factor analysis, because of this fact, validating factor analysis has been conducted in this research. 5 points in the “Scale” has been disapproved and removed at the end of validating factor analysis. The validity of the internal sequence of the “Scale” has been calculated with the use of Cronbach Alpha coefficient. The validity ratio of the subfactors of the “Scale” has been calculated as 0.92 for entrepreneurship and effective communication, 0.94 for innovation and changes and 0.76 for variety. This research concludes that “Scale of The Creative Leadership Qualities of School Administrators” is valid and accurate in case of Azerbaijan. Key words: school administrator, creative leadership, “Scale”, validity, accuracy

ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29

Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linked ERAP2 with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labeled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.

Target spike patterns enable efficient and biologically plausible learning for complex temporal tasks

Recurrent spiking neural networks (RSNN) in the brain learn to perform a wide range of perceptual, cognitive and motor tasks very efficiently in terms of energy consumption and their training requires very few examples. This motivates the search for biologically inspired learning rules for RSNNs, aiming to improve our understanding of brain computation and the efficiency of artificial intelligence. Several spiking models and learning rules have been proposed, but it remains a challenge to design RSNNs whose learning relies on biologically plausible mechanisms and are capable of solving complex temporal tasks. In this paper, we derive a learning rule, local to the synapse, from a simple mathematical principle, the maximization of the likelihood for the network to solve a specific task. We propose a novel target-based learning scheme in which the learning rule derived from likelihood maximization is used to mimic a specific spatio-temporal spike pattern that encodes the solution to complex temporal tasks. This method makes the learning extremely rapid and precise, outperforming state of the art algorithms for RSNNs. While error-based approaches, (e.g. e-prop) trial after trial optimize the internal sequence of spikes in order to progressively minimize the MSE we assume that a signal randomly projected from an external origin (e.g. from other brain areas) directly defines the target sequence. This facilitates the learning procedure since the network is trained from the beginning to reproduce the desired internal sequence. We propose two versions of our learning rule: spike-dependent and voltage-dependent. We find that the latter provides remarkable benefits in terms of learning speed and robustness to noise. We demonstrate the capacity of our model to tackle several problems like learning multidimensional trajectories and solving the classical temporal XOR benchmark. Finally, we show that an online approximation of the gradient ascent, in addition to guaranteeing complete locality in time and space, allows learning after very few presentations of the target output. Our model can be applied to different types of biological neurons. The analytically derived plasticity learning rule is specific to each neuron model and can produce a theoretical prediction for experimental validation.

ERAP2 facilitates a subpeptidome of Birdshot Uveitis-associated HLA-A29

ABSTRACTBirdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linked ERAP2 with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labelled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.

Remarks on syllable structure and metrical structure in Biblical Hebrew

In the Middle Ages Biblical Hebrew was transmitted in a variety of oral reading traditions, which became textualized in systems of vocalization signs. The two most important oral traditions were the Tiberian and the Babylonian, which were represented by different vocalization sign systems. These two oral traditions had their origins in ancient Palestine. Although closely related, they exhibit several differences. These include differences in syllable and metrical structure. This paper examines how the syllable and metrical structure of the two traditions reflected by the medieval vocalization sign systems should be reconstructed. The Tiberian tradition exhibits an ‘onset typology’ of syllabification, where word-internal /CCC/ clusters are syllabified /C.CC/ and word-initial clusters are syllabified within the onset /CC-/. The Babylonian tradition exhibits a right-to-left computation of syllables resulting in a ‘coda typology,’ whereby the second consonant of a word-internal sequence /CCC/ is syllabified as a coda, viz. /CC.C/, and word-initial clusters are syllabified C.C, with the first consonant extra-syllabic.

Biological Plasticity Rescues Target Activity in CRISPR Knockouts

Gene knockouts (KOs) are efficiently engineered through CRISPR-Cas9-induced frameshift mutations. While DNA editing efficiency is readily verified by DNA sequencing, a systematic understanding of the efficiency of protein elimination has been lacking. Here, we devised an experimental strategy combining RNA-seq and triple-stage mass spectrometry (SPS-MS3) to characterize 193 genetically verified deletions targeting 136 distinct genes generated by CRISPR-induced frameshifts in HAP1 cells. We observed residual protein expression for about one third of the quantified targets, at variable levels from low to original, and identified two causal mechanisms, translation reinitiation leading to N-terminally truncated target proteins, or skipping of the edited exon leading to protein isoforms with internal sequence deletions. Detailed analysis of three truncated targets, BRD4, DNMT1 and NGLY1, revealed partial preservation of protein function. Our results imply that systematic characterization of residual protein expression or function in CRISPR-Cas9 generated KO lines is necessary for phenotype interpretation.

Molecular characteristics of serum hepatitis B virus (HBV) RNA: a novel biomarker for chronic HBV infection

Background and Hypothesis: HBV is a major etiological agent for viral hepatitis and hepatocellular carcinoma. HBV is a DNA virus per se but viral pregenomic RNA (pgRNA) has been recently found in patient blood. The serum pgRNA is hypothesized to function as a novel biomarker for the activity of HBV covalently- closed-circular DNA (cccDNA), which is the intracellular persistent form of HBV DNA and the template for producing viral proteins responsible for the chronic virulence of HBV. However, the molecular characteristics of serum HBV RNA remains elusive. Experimental Design and Project Methods: HBV RNA were extracted from patient’s sera. RT-PCR and 3’ RACE were utilized to amplify the internal sequence and 3’ terminus of HBV pgRNA, respectively. The PCR products were gel purified and cloned into T vector for sequencing. Results: After comparing the sequencing data to the reference HBV sequence, we found that the serum HBV RNA are spliced fragments of the original intracellular full-length pgRNA. The prevalence of the fragmented serum pgRNA was found in greater concentrations in untreated patients, and the ratios of different spliced forms of serum HBV RNA vary during the course of antiviral treatment. Conclusion and Potential Impact: Our study demonstrated that the serum HBV RNA are spliced/truncated forms of pgRNA, indicating that the RNA-containing virion is noninfectious. The characterization of serum HBV RNA sequence provides important insights into the assay design for serum HBV RNA detection. Future study will focus on the mechanism underlying the selective egress of spliced pgRNA-containing virus particles.

Pentatricopeptide repeat poly(A) binding protein from mitochondria of trypanosomes

In Trypanosoma brucei, most mitochondrial mRNAs undergo U-insertion/deletion editing, and 3′ adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: Pre-editing addition of the short (A) tail protects the edited transcript against 3′-5′ degradation, while post-editing A/U-tailing renders mRNA competent for ribosome recruitment. Participation of a poly(A) binding protein (PABP) in coupling of editing and 3′ modification processes has been inferred, but its identity and mechanism of action remained elusive. We report identification of KPAF4, a pentatricopeptide repeat-containing PABP which sequesters the A-tail and impedes exonucleolytic degradation. Conversely, KPAF4 inhibits uridylation of A-tailed transcripts and, therefore, premature A/U-tailing of partially-edited mRNAs. This quality check point prevents translation of incompletely edited mRNAs. Our findings also implicate the RNA editing substrate binding complex (RESC) in mediating the interaction between the 5′ end bound pyrophosphohydrolase MERS1 and 3′ end associated KPAF4 to enable mRNA circularization. This event is critical for transcript stability during the editing process.