Deletion Patterns Research Articles

The MICA deletion across different populations

The MICA gene encodes a glycoprotein upregulated upon cellular stress, particularly in oxidative stress, intracellular infections, and tumorigenesis. This stress-signaling molecule interacts with the activating receptor NKG2D from Natural Killer (NK) and some T lymphocytes, stimulating their cytotoxic activity. MICA is encoded within the human Major Histocompatibility Complex next to the HLA-B locus and is highly polymorphic. MICA might be absent from chromosome 6 due to a large deletion of approximately 100 Kb between HLA-B and MICB. Therefore, some individuals may not produce any isoform of MICA. The distribution of this phenotype may vary among different populations. We evaluated the distribution of the MICA*del and other MICA null alleles in different biogeographic regions and the Linkage Disequilibrium (LD) pattern between this allele and HLA-B. We detected at least two different patterns of deletion, one with full deletion of MICA and surrounding sequences and one partial MICA deletion. The presence of different patterns of deletion suggests independent deletion events. We confirm that the previously described MICA*del allele is mainly associated with B*48 and MICB*009N in Asia and America, but other haplotypes also occur. While most samples with complete or partial MICA deletion are heterozygous and present one functional copy of both MICA and MICB genes, we detected two samples with no functional MICA and one with no functional MIC genes. Therefore, other mechanisms might be in place to compensate for the absence of MIC molecules.

Study on the influence of the sY1192 gene locus in the AZFb/c region on sperm quality and pregnancy outcome.

Y chromosome microdeletions are an important cause of male infertility. At present, research on the Y chromosome is mainly focused on analyzing the loss of large segments of the azoospermia factor a/b/c (AZFa/b/c) gene, and few studies have reported the impact of unit point deletion in the AZF band on fertility. This study analyzed the effect of sperm quality after sY1192 loss in 116 patients. The sY1192-independent deletion accounted for 41.4% (48/116). Eight patterns were found in the deletions associated with sY1192. The rate of sperm detection was similar in the semen of patients with the independent sY1192 deletion and the combined sY1192 deletions (52.1% vs 50.0%). The patients with only sY1192 gene loss had a higher probability of sperm detection than the patients whose sY1192 gene locus existed, but other gene loci were lost (52.1% vs 32.0%). The hormone levels were similar in patients with sY1192 deletion alone and in those with sY1192 deletion and other types of microdeletions in the presence of the sY1192 locus. After multiple intracytoplasmic sperm injection (ICSI) attempts, the pregnancy rate of spouses of men with sY1192-independent deletions was similar to that of other types of microdeletions, but the fertilization and cleavage rates were higher. We observed that eight deletion patterns were observed for sY1192 microdeletions of AZFb/c, dominated by the independent deletion of sY1192. After ICSI, the fertilization rate and cleavage rate of the sY1192-independent microdeletion were higher than those of other Y chromosome microdeletion types, but there was no significant difference in pregnancy outcomes.

Context effects on repair of 5'-overhang DNA double-strand breaks induced by Cas12a in Arabidopsis.

Sequence-specific endonucleases have been key to the study of the mechanisms and control of DNA double-strand break (DSB) repair and recombination, and the availability of CRISPR-Cas nucleases over the last decade has driven rapid progress in the understanding and application of targeted recombination in many organisms, including plants. We present here an analysis of recombination at targeted chromosomal 5' overhang DSB generated by the FnCas12a endonuclease in the plant, Arabidopsis thaliana. The much-studied Cas9 nuclease cleaves DNA to generate blunt-ended DSBs, but relatively less is known about the repair of other types of breaks, such as those with 5'-overhanging ends. Sequencing the repaired breaks clearly shows that the majority of repaired DSB carry small deletions and are thus repaired locally by end-joining recombination, confirmed by Nanopore sequencing of larger amplicons. Paired DSBs generate deletions at one or both cut-sites, as well as deletions and reinsertions of the deleted segment between the two cuts, visible as inversions. While differences are seen in the details, overall the deletion patterns are similar between repair at single-cut and double-cut events, notwithstanding the fact that only the former involve cohesive DNA overhangs. A strikingly different repair pattern is however observed at breaks flanked by direct repeats. This change in sequence context results in the presence of a major alternative class of repair events, corresponding to highly efficient repair by single-strand annealing recombination.

Acquisition of Gutturals by Ammani-Jordanian Arabic-Speaking Preschoolers.

This study aims at investigating the phonological development of the six guttural consonants of Jordanian Arabic, /χ/, /ʁ/, /ħ/, /ʕ/, /ʔ/, and /h/. An articulation test is designed to involve two tasks: picture naming and repetition. The test includes 54 words for picture naming and 18 words for repetition, representing all possible positions of the targeted guttural sounds. Samples are collected from 40 typically developing Ammani-Jordanian Arabic-speaking monolingual children, living in Amman, Jordan. Respondents are equally divided into eight age-related trajectories: 2-2;6, 2;6-3, 3-3;6, 3;6-4, 4-4;6, 4;6-5, 5-5;6, and 5;6-6 (years;months). No child with a history of hearing, speech, or vision disorders is included. The data are analyzed using production accuracy, where the three developmental trajectories of production (customary, acquisition, and mastery) are determined for each guttural, and error analysis, addressed based on perceptual judgments, providing details of every mispronounced or deleted guttural. The results show that /χ/, /ħ/, /ʕ/, and /ʔ/ are acquired before the age of 6 years, while /ʁ/ and /h/ are still not acquired by this age. Respondents use relatively variant alternatives for the mispronounced cognates, including guttural, nonguttural sounds, and vowel substitution. The /ʁ/ is the guttural with the highest number of alternatives, while /ʔ/ gets the least. The analysis also reveals patterns of guttural deletion, with variations across different guttural sounds and positions. Despite errors/deviations made, respondents score accuracy percentages that gradually increase in correlation with age. The guttural /ʁ/ starts with the lowest accuracy percentages, while /ʔ/ and /ħ/ start with the highest. These findings illuminate on the developmental trajectory of guttural acquisition and enrich our understanding of children's evolving perception and production abilities. They offer valuable insights into the patterns of guttural sound production in Jordanian Arabic-speaking children, laying the groundwork for further research and the development of targeted assessment and intervention strategies to support phonological development in this population.

Genotypic characterization of novel S-DEL variants of porcine epidemic diarrhea virus identified in South Korea.

The highly pathogenic genotype 2b (HP-G2b) of porcine epidemic diarrhea virus (PEDV), which caused a pandemic in 2013-2014, evolved in South Korea and became endemic, affecting the domestic pig industry. This study describes the genotypic traits of novel HP-G2b PEDV strains identified on affected farms experiencing low disease severity with < 10% neonatal mortality. Nucleotide sequencing revealed common deletion patterns, termed S-DEL2, resulting in a two-amino-acid deletion at positions 60 and 61, 61 and 62, or 63 and 64 in the N-terminal domain of the spike (S) protein of all isolates. The S barcode profiles of S-DEL2 variants differed from each other and shared 96.0-99.4% and 98.5-99.6% nt sequence identity with other South Korean HP-G2b PEDV strains in the S gene and in the complete genome sequence, respectively. Genetic and phylogenetic analysis showed that the S-DEL2 strains belonged to diverse domestic clades: CK, CK.1, CK.2, or NC. The emergence of novel S-DEL2 strains suggests that continuous evolution of PEDV occurs under endemic circumstances, resulting in genetic diversity and distinct clinical presentations. This study advances our knowledge regarding the genetic and pathogenic heterogeneity of PEDV and emphasizes the importance of active monitoring and surveillance to identify novel variants and determine their genotypic and phenotypic characteristics.

Molecular epizootiology of porcine reproductive and respiratory syndrome virus in the Xinjiang Uygur Autonomous Region of China.

Rapid evolution of porcine reproductive and respiratory syndrome virus (PRRSV) is the bottleneck for effective prevention and control of PRRS. Thus, understanding the prevalence and genetic background of PRRSV strains in swine-producing regions is important for disease prevention and control. However, there is only limited information about the epizootiological situation of PRRS in the Xinjiang Uygur Autonomous Region, China. In this study, blood or lung tissue samples were collected from 1,411 PRRS-suspected weaned pigs from 9 pig farms in Changji, Shihezi, and Wujiaqu cities between 2020 and 2022. The samples were first tested by RT-quantitative PCR, yielding a PRRSV-2 positive rate of 53.6%. Subsequently, 36 PRRSV strains were isolated through initial adaptation in bone marrow-derived macrophages followed by propagation in grivet monkey Marc-145 cells. Furthermore, 28 PRRSV-positive samples and 20 cell-adapted viruses were selected for high-throughput sequencing (HTS) to obtain the entire PRRSV genome sequences. Phylogenetic analysis based on the nucleotide sequences of the ORF5 gene of the PRRSV strains identified in this study grouped into sub-lineages 1.8 and 8.7 the former being the dominant strain currently circulating in Xinjiang. However, the NSP2 proteins of the Xinjiang PRRSV strains shared the same deletion patterns as sub-lineage 1.8 prototype strain NADC30 with the exception of 4 strains carrying 2-3 additional amino acid deletions. Further analysis confirmed that recombination events had occurred in 27 of 37 PRRSVs obtained here with the parental strains belonging to sub-lineages 1.8 and 8.7, lineages 3 and 5, with the recombination events having occurred most frequently in the 5' and 3' termini of ORF1a and 5' terminus of ORF1b.

Characterization and Pathogenicity of the Novel Porcine Reproductive and Respiratory Syndrome Virus 1 Strain SL-01 in China

Currently, PRRSV-1 causes a large number of clinical infections in Chinese swine herds, and the prevalence of new strains has presented great challenges. In this study, the novel PRRSV-1 strain SL-01 was isolated, with a genome length of 14,978 bp, and genetic evolution analysis revealed that it belonged to a new subtype branch. Sequence homology analysis showed that the strain was only 82.2%–86.7% identical to the current classical PRRSV-1 strains. In particular, the novel strain exhibited a unique deletion pattern in Nsp2. In addition, GP3 and GP4 of the SL-01 strain showed four consecutive amino acid deletions in the highly variable regions at amino acids 243–248 and 63–68, respectively. Further challenges in piglet and pregnant sow demonstrated that the SL-01 strain could cause the piglet fever and death but less pathogenic to pregnant sow. Overall, the characterization and pathogenicity of a novel PRRSV-1 strain were first explored and provide a prevention for pig farms.

Efficacy of atoxigenic Aspergillus flavus from southern China as biocontrol agents against aflatoxin contamination in corn and peanuts

Aspergillus flavus is a ubiquitous facultative pathogen that routinely infects important crops leading to formation of aflatoxins during crop development and after harvest. Corn and peanuts in warm and/or drought-prone regions are highly susceptible to aflatoxin contamination. Controlling aflatoxin using atoxigenic A. flavus is a widely adopted strategy. However, no A. flavus genotypes are currently approved for use in China. The current study aimed to select atoxigenic A. flavus endemic to Guangxi Zhuang Autonomous Region with potential as active ingredients of aflatoxin biocontrol products. A total of 204 A. flavus isolates from corn, peanuts, and field soil were evaluated for ability to produce the targeted mycotoxins. Overall, 57.3% could not produce aflatoxins while 17.15% were incapable of producing both aflatoxins and CPA. Atoxigenic germplasm endemic to Guangxi was highly diverse, yielding 8 different gene deletion patterns in the aflatoxin and CPA biosynthesis gene clusters ranging from no deletion to deletion of both clusters. Inoculation of corn and peanuts with both an aflatoxin producer and selected atoxigenic genotypes showed significant reduction (74 to 99%) in aflatoxin B1 (AFB1) formation compared with inoculation with the aflatoxin producer alone. Atoxigenic genotypes also efficiently degraded AFB1 (61%). Furthermore, atoxigenic isolates were also highly efficient at reducing aflatoxin concentrations even when present at lower concentrations than aflatoxin producers. The use of multiple atoxigenics was not always as effective as the use of a single atoxigenic. Effective atoxigenic genotypes of A. flavus with known mechanisms of atoxigenicity are demonstrated to be endemic to Southern China. These A. flavus may be utilized as active ingredients of biocontrol products without concern for detrimental impacts that may result from introduction of exotic fungi. Field efficacy trials in the agroecosystems of Southern China are needed to determine the extent to which such products may allow the production of safer food and feed.

Transition mutation bias is crucial to adaptive extended spectrum beta lactamase (ESBL) resistance evolution

The importance of slow accumulation of mutation in the nucleic acids of bacteria and the possibility of organismal transcriptional modification to suit their adaptation are key drivers favouring natural selection and subsequently adaptive evolution. This study was aimed at providing insight into factors influencing adaptive extended spectrum beta lactamase (ESBL) resistance evolution. A total of twenty-six (26) extended spectrum beta lactamase-producing Gram-negative bacteria isolated in our previous study were subjected to uniplex and multiplex polymerase chain reaction (PCR) and sequencing prior to mutation discovery analyses, while the maximum likelihood value, transition-transversion ratio, tajimas neutrality test, nucleotide diversity and selection analyses were estimated following standard recommended protocols. Results obtained depict the PCR discriminated ESBL alleles as; TEM (n = 11.5 %), CTX-M (n = 15.4 %), SHV (n = 19.2 %) while the co-occurred ESBL alleles were estimated as CTX-M and TEM (n = 3.85 %), CTX-M and SHV (n = 15.4 %), TEM and SHV (n = 23.1 %), CTX-M, TEM and SHV (n = 11.5 %). The transition, transversion, deletion and insertion distribution pattern were evaluated as; TEM (46, 39,11 and 4 %), SHV (50, 31, 8 and 11 %) and CTX-M (60, 21,12 and 7 %) (p < 0.05) respectively. The maximum likelihood value, transition-transversion ratio, tajimas neutrality test, nucleotide diversity and selection analyses for TEM, SHV and CTX-M were (−8436, 1.18, 5.2, 62 % and 84.9 %,), (−8321, 1.60, 5.4, 68.9 % and 97.8 %) and (−7284, 2.86, 6.0, 55.2 % and 77.2 %) sequentially. Our findings therefore have shown that adaptive ESBL resistance evolution is driven by transition mutation, positive natural selection and ESBL gene flow. It is thus imperative to state that understanding these adaptive resistance driven factors and how they operate is crucial to deciphering the fundamental principles of adaptive evolution that might help circumvent the global challenges of antibiotic resistance.

Investigation of cuproptosis regulator-mediated modification patterns and SLC30A7 function in GBM.

Copper-dependent controlled cell death (cuproptosis) is a novel cell death modality that is distinct from known cell death mechanisms. Nonetheless, the potential role of the cuproptosis regulator in tumour microenvironment (TME) of GBM remains unknown. Based on 13 widely recognised cuproptosis regulators, the cuproptosis regulation patterns and the biological characteristics of each pattern were comprehensively assessed in GBMs. Machine learning strategies were used to construct a CupScore to quantify the cuproptosis regulation patterns of individual tumours. A PPI network was constructed to predict core-associated genes of cuproptosis regulators. The function of the novel cuproptosis regulators SLC30A7 was examined by in vitro and in vivo experiment. We identified three distinct cuproptosis regulation patterns, including immune activation, metabolic activation, and immunometabolic double deletion patterns. The CupScore was shown to predict the abundance of tumour inflammation, molecular subtype, stromal activity, gene variation, signalling pathways, and patient prognosis. The low CupScore subtype was characterised by immune activation, isocitrate dehydrogenase mutations, sensitivity to chemotherapy, and clinical benefits. The high CupScore subtype was characterised by activation of the stroma and metabolism and poor survival. Novel cuproptosis regulator SLC30A7 knockdown inhibited the cuproptosi via JAK2/STAT3/ATP7A pathway in GBM. Cuproptosis regulators have been shown to play a vital role in TME complexity. Constructing CupScores were trained to evaluate the regulation patterns of cuproptosis in individual tumours. The novel cuproptosis-related genes SLC30A7 was involved in regulation the tumorigenicity of GBM cell via JAK2/STAT3/ATP7A pathway in vitro and in vivo.

Isolation, identification, recombination analysis and pathogenicity experiment of a PRRSV recombinant strain in Sichuan Province, China.

Since 2013, the porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2), lineage 1.8 (NADC30-like PRRSV) has emerged and become widely prevalent in China. The NADC30-like PRRSV poses significant challenges for disease control, primarily because of its propensity for frequent mutations and recombinations. We successfully isolated and identified a NADC30-like strain, designated SCCD22, in Chengdu, Sichuan Province, China. We meticulously examined the genetic recombination properties and evaluated its pathogenicity in 28-day-old piglets. SCCD22 showed 93.02% nucleotide homology with the NADC30 PRRSV strain, and its non-structural protein 2 coding region showed the same 131 amino acid deletion pattern as that seen in NADC30. Furthermore, we identified two recombination events in SCCD22: one in the NSP2 region (1,028-3,290 nt), where it was highly similar to the JXA1-like strain GZ106; and another in the NSP10 ~ 12 region (9,985-12,279 nt), closely resembling the NADC30-like strain CY2-1604. Piglets infected with SCCD22 exhibited clinical symptoms such as elevated body temperature, prolonged fever, reduced appetite, and roughened fur. Postmortem examinations underscored the typical lung pathology associated with PRRSV, indicating that the lungs were the primary affected organs. Furthermore, extended viral shedding accompanied by progressive viremia was observed in the serum and nasal excretions of infected piglets. In summary, this study reports a domestic PRRSV recombination strain in the Sichuan Province that can provide critical insights into preventing and controlling PRRSV in this region.

Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak.

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a serious threat to the pig industry in China. Our previous study demonstrated that PRRSV persists with local circulations and overseas imports in China and has formed a relatively stable epidemic pattern. However, the sudden African swine fever (ASF) outbreak in 2018 caused serious damage to China's pig industry structure, which resulted in about 40 per cent of pigs being slaughtered. The pig yields recovered by the end of 2019. Thus, whether the ASF outbreak reframed PRRSV evolution with changes in pig populations and further posed new threats to the pig industry becomes a matter of concern. For this purpose, we conducted genomic surveillance and recombination, NSP2 polymorphism, population dynamics, and geographical spread analysis of PRRSV-2, which is dominant in China. The results showed that the prevalence of ASF had no significant effects on genetic diversities like lineage composition, recombination patterns, and NSP2 insertion and deletion patterns but was likely to lead to changes in PRRSV-2 recombination frequency. As for circulation of the two major sub-lineages of Lineage 1, there was no apparent transmission of NADC30-like among provinces, while NADC34-like had obvious signs of inter-provincial transmission and foreign importation during the ASF epidemic. In addition, two suspected vaccine recombinant epidemic strains suggest a slight safety issue of vaccine use. Herein, the interference of ASF to the PRRSV-2 evolutionary pattern was evaluated and vaccine safety was analyzed, in order to monitor the potential threat of PRRSV-2 to China's pig industry in the post-epidemic era of ASF.

Telomere-to-telomere genome assembly of the aflatoxin biocontrol agent Aspergillus flavus isolate La3279 isolated from maize in Nigeria.

Here, we report the complete genome of the non-aflatoxigenic Aspergillus flavus isolate La3279, which is an active ingredient of the aflatoxin biocontrol product Aflasafe. The chromosome-scale assembly clarifies the deletion pattern in the aflatoxin biosynthesis gene cluster and corrects a misidentified assembly previously published for this isolate.

Novel Tree Shrew Cytochrome P450 2Ds (CYP2D8a and CYP2D8b) Are Functional Drug-Metabolizing Enzymes that Metabolize Bufuralol and Dextromethorphan.

Tree shrews are a nonprimate species used in a range of biomedical studies. Recent genome analysis of tree shrews found that the sequence identities and the numbers of genes of cytochrome P450 (CYP or P450), an important family of drug-metabolizing enzymes, are similar to those of humans. However, tree shrew P450s have not yet been sufficiently identified and analyzed. In this study, novel CYP2D8a and CYP2D8b cDNAs were isolated from tree shrew liver and were characterized, along with human CYP2D6, dog CYP2D15, and pig CYP2D25. The amino acid sequences of these tree shrew CYP2Ds were 75%-78% identical to human CYP2D6, and phylogenetic analysis showed that they were more closely related to human CYP2D6 than rat CYP2Ds, similar to dog and pig CYP2Ds. For tree shrew CYP2D8b, two additional transcripts were isolated that contained different patterns of deletion. The gene and genome structures of CYP2Ds are generally similar in dogs, humans, pigs, and tree shrews. Tree shrew CYP2D8a mRNA was most abundantly expressed in liver, among the tissue types analyzed, similar to dog CYP2D15 and pig CYP2D25 mRNAs. Tree shrew CYP2D8b mRNA was also expressed in liver, but at a level 7.3-fold lower than CYP2D8a mRNA. Liver microsomes and recombinant protein of both tree shrew CYP2Ds metabolized bufuralol and dextromethorphan, selective substrates of human CYP2D6, but the activity level of CYP2D8a greatly exceeded that of CYP2D8b. These results suggest that tree shrew CYP2D8a and CYP2D8b are functional drug-metabolizing enzymes, of which CYP2D8a is the major CYP2D in liver. SIGNIFICANCE STATEMENT: Novel tree shrew CYP2D8a and CYP2D8b cDNAs were isolated from liver. Their amino acid sequences were 75%-78% identical to human CYP2D6. For CYP2D8b, two additional transcripts contained different patterns of deletion. Tree shrew CYP2D8a mRNA was abundantly expressed in liver, similar to dog CYP2D15 and pig CYP2D25 mRNAs. Recombinant tree shrew CYP2Ds catalyzed the oxidation of bufuralol and dextromethorphan. Tree shrew CYP2D8a and CYP2D8b are functional drug-metabolizing enzymes, of which CYP2D8a is the major CYP2D in liver.

The Spectrum of Deletion Pattern in the Dystrophin Gene in Duchenne Muscular Dystrophy Patients: A Cross-sectional Study from Northeast India

Introduction: Duchenne Muscular Dystrophy (DMD) is an X-linked recessive neuromuscular disorder characterised by progressive, irreversible muscle weakness. It is caused by a mutation in the dystrophin or DMD gene, leading to the absence of the essential muscle protein Dystrophin in DMD. Muscle strength continually diminishes, and death usually occurs from chronic respiratory insufficiency and/or cardiac failure. Due to the high mortality rate, early diagnosis is crucial to allow appropriate planning for patient care and treatment. In India, the traditional multiplex Polymerase Chain Reaction (PCR) assay is the most common method to detect Dystrophin gene deletion mutations. Aim: To describe the spectrum of deletion patterns in the dystrophin gene in muscular dystrophy patients attending a tertiary care hospital in Northeast India. Materials and Methods: A hospital-based cross-sectional study was conducted on a total of 53 suspected DMD patients attending the Department of Neurology and Department of Paediatrics at Assam Medical College, Dibrugarh, Assam, India from January 2016 to December 2022. Multiplex PCR was performed to study the deletion patterns for the 25 most common exons of the DMD gene for all patients at the Genetic lab, Department of Anatomy. Deletion mutations at different multiple exons were found, and the results were statistically analysed using Statistical Package for Social Sciences (SPSS) to calculate the mean and standard deviation. The results were presented in tabular form as percentages. Results: Out of the 53 cases suspected to have DMD on the basis of clinical presentation and high serum Creatine Kinase (CK) levels, 34 patients (64.2%) showing deletion mutations in the 25 most common exons of the DMD gene were included in the study. Deletions were most common in 15 (44.1%) patients in the distal hotspot region of exons 44-55. The most common gene deleted was exon 50 in 11 (32.4%) patients. The age at which symptoms were noticed was 4.7±2.01 years. The mean age at diagnosis was 8.4±2.4 years. Conclusion: In the present study, most patients suspected of DMD based on clinical and laboratory findings had deletions in the DMD gene, with the most common region for deletion in the dystrophin gene being the distal hotspot region, and exon 50 being the most commonly deleted.

WHY DO ARAB-PALESTINIAN JOURNALISTS DELETE TWEETS?

In Israel and Palestine, as in many countries, the majority of journalists operate an account on Twitter for different purposes, from news gathering and reporting to attracting new audiences and maintaining a relationship with their readers (Hanusch &amp; Bruns, 2017). Many studies of Twitter’s journalistic role have examined journalists’ tweeting practices and the ways in which Twitter serves as an organizational and individual branding tool (e.g., Molyneux, Holton, &amp; Lewis, 2018). However, only a few studies have examined the patterns of tweet deletion among journalists. Ringel and Davidson (2022) conceptualized the practice of tweet deletion as an instance of “proactive ephemerality, a social media phenomenon that occurs when users intentionally remove their own content from their social media profiles manually or with the aid of mechanical tools” (p. 1218). In this study, we examine the motivations of Arab-Palestinian journalists who operate in Israel for deleting their tweets. Based on semi-structured interviews with Arab-Palestinian journalists working in Israel, we seek to understand why they proactively erase tweets. Further, we wish to consider the implications of such an act for Twitter’s functioning as a public record.

Increasing deletion sizes and the efficiency of CRISPR/Cas9-mediated mutagenesis by SunTag-mediated TREX1 recruitment.

Previously, it has been shown that mutagenesis frequencies can be improved by directly fusing the human exonuclease TREX2 to Cas9, resulting in a strong increase in the frequency of smaller deletions at the cut site. Here, we demonstrate that, by using the SunTag system for recruitment of TREX2, the mutagenesis efficiency can be doubled in comparison to the direct fusion in Arabidopsis thaliana. Therefore, we also tested the efficiency of the system for targeted deletion formation by recruiting two other 3'-5' exonucleases, namely the human TREX1 and E. coli ExoI. It turns out that SunTag-mediated recruitment of TREX1 not only improved the general mutation induction efficiency slightly in comparison to TREX2, but that, more importantly, the mean size of the induced deletions was also enhanced, mainly via an increase of deletions of 25 bp or more. EcExoI also yielded a higher amount of larger deletions. However, only in the case of TREX1 and TREX2, the effect was predominately SunTag-dependent, indicating efficient target-specific recruitment. Using SunTag-mediated TREX1 recruitment at other genomic sites, we were able to obtain similar deletion patterns. Thus, we were able to develop an attractive novel editing tool that is especially useful for obtaining deletions in the range from 20 to 40 bp around the cut site. Such sizes are often required for the manipulation of cis-regulatory elements. This feature is closing an existing gap as previous approaches, based on single nucleases or paired nickases or nucleases, resulted in either shorter or longer deletions, respectively.

The clinical, myopathological, and genetic analysis of 155 Chinese mitochondrial ophthalmoplegia patients with mitochondrial DNA single large deletions.

Progressive external ophthalmoplegia (PEO) is a common subtype of mitochondrial encephalomyopathy. The study aimed to investigate the relationship between mitochondrial DNA (mtDNA) abnormalities, muscle pathology, and clinical manifestations in Chinese patients with single large-scale mtDNA deletion presenting with PEO. This is a retrospective single-center study. Patients with PEO who had a single large deletion in mitochondrial DNA were included in this study. The associations were analyzed between mtDNA deletion patterns, myopathological changes, and clinical characteristics. In total, 155 patients with mitochondrial PEO carrying single large-scale mtDNA mutations were enrolled, including 137 chronic progressive external ophthalmoplegia (CPEO) and 18 Kearns-Sayre syndrome (KSS) patients. The onset ages were 9.61 ± 4.12 in KSS and 20.15 ± 9.06 in CPEO. The mtDNA deletions ranged from 2225 bp to 9131 bp, with m.8470_13446del being the most common. The KSS group showed longer deletions than the CPEO group (p = 0.004). Additionally, a higher number of deleted genes encoding respiratory chain complex subunits (p = 0.001) and tRNA genes (p = 0.009) were also observed in the KSS group. A weak negative correlation between the mtDNA deletion size and ages of onset (p < 0.001, r = -0.369) was observed. The proportion of ragged red fibers, ragged blue fibers, and cytochrome c negative fibers did not correlate significantly with onset ages (p > 0.05). However, a higher percentage of abnormal muscle fibers corresponds to an increased prevalence of exercise intolerance, limb muscle weakness, dysphagia, and cerebellar ataxia. We reported a large Chinese cohort consisting of mitochondrial PEO patients with single large-scale mtDNA deletions. Our results demonstrated that the length and locations of mtDNA deletions may influence onset ages and clinical phenotypes. The severity of muscle pathology could not only indicate diagnosis but also may be associated with clinical manifestations beyond the extraocular muscles.

Identification of data wiping tools based on deletion patterns in ReFS $Logfile

Data wiping tools permanently delete files by repeatedly overwriting data on a digital device, making file recovery impossible. Unlike the conventional deletion methods, which merely remove the file system pointer to the data, these tools are designed to entirely and irretrievably erase the data. This method can be exploited to obliterate evidence of a crime. Given the growing prevalence of such tools, a comprehensive analysis of permanent deletion behavior is essential, especially concerning the Resilient File System (ReFS). In this study, we propose a method for detecting user behavior concerning data wiping tools and algorithms in ReFS 3.7. Our approach relies on the fact that file modifications are logged in the redo record of the $Logfile, and that the opcode value of the redo record varies depending on the data wiping tool used. Since opcodes were only analyzed up to version 3.4, we analyzed the newly updated opcodes. Initially, we selected the 12 most commonly used data wiping tools for our research. In the pattern analysis phase, we applied the algorithms supported by each tool, generating a distinct deletion pattern for each one. This was accomplished by utilizing consecutive opcodes to formulate the patterns and monitor transitions in file and directory names. The patterns discerned in the $Logfile allowed us to determine which data wiping tool was deployed. The proposed methodology simplifies the identification of not only which data wiping tool has been used, but also the specific deletion behavior exhibited. We developed a tool incorporating the proposed method. Our subsequent verification confirmed the effectiveness of our methodology and tools in accurately detecting the use of comprehensive deletion tools. These findings contribute valuable insights to the acquisition of digital evidence of user deletion behavior in ReFS. Our proposed methodology will help digital forensic examiners in the detection and identification of data wiping tools' behavior.

A-145 Development of a Novel Algorithm Using Red Blood Cell Indices for Screening of Alpha Globin Gene Deletions

Abstract Background Distinguishing between different causes of microcytic anemia is essential for management of anemic patients. More than 20 different RBC indices have been used to screen thalassemia trait with inconsistent results. Differentiation between iron deficiency anemia (IDA) and alpha-thalassemia is challenging based on RBC indices alone. Moreover, thalassemia and IDA may coexist. A highly sensitive screening algorithm is needed to select clinical cases for alpha globin gene analysis to reduce unnecessary testing and improve pre-test probabilities. Methods A retrospective study was performed to evaluate the reliability of 22 RBC indices (RBC, MCV, RDW, MCH, Mentzer Index, RDW Index, etc) and formulae in differentiating cases with 1–2 alpha globin gene deletions from negative cases, in a cohort of 90 individuals with confirmatory alpha globin gene analysis results. Results The number of patients with each alpha globin gene deletion pattern were: 37 patients with alpha-thalassemia trait, 21 silent carriers (one gene deletion), 31 patients with negative result and 1 patient with triplicated alpha globin gene. The mean RBC count in each group were 4.79 ± 0.65 (trait), 4.45 ± 0.73 (carrier), and 4.21 ± 0.84 (negative) (million/mm). The mean MCV in each group were 71.1 ± 4.8 (trait), 76.1 ± 5.9 (carrier), and 74.2 ± 9.3 (negative) (fL). The mean RDW in each group were 16.5 ± 3.0 (trait), 17.2 ± 3.4 (carrier), and 18.3 ± 4.9 (negative) (%). The mean MCH in each group were 22.0 ± 1.8 (trait), 23.8 ± 2.3 (carrier), and 23.5 ± 3.7 (negative) (pg). None of the RBC indices showed significant difference between carrier and negative groups, while 20 RBC indices showed significant difference (P &amp;lt; 0.05) between trait and negative groups. The sensitivities of the RBC indices in detecting 1–2 alpha globin gene deletions based on published cut-offs ranged between 3.4% and 81.0%, while the specificities ranged between 41.9% and 100%. A novel scoring algorithm was evaluated based on the combination of 12 selected RBC indices and formulae, with each index or formula contributing to a score of 0 or 1. The average value of the negative cases was used as the score cut-off value for each index or formula. The scoring algorithm gave a score distribution between 0 and 12, with lower scores indicating alpha globin gene deletions. It achieved a sensitivity of 96.6% in detecting 1–2 alpha globin gene deletions, with a negative likelihood ratio of 0.15. The negative likelihood ratio of the scoring algorithm outperformed each of the individual RBC indices at similar levels of sensitivities (&amp;gt;95%). Conclusion The novel algorithm is a highly sensitive tool for screening of alpha globin gene deletions, including one gene deletion. It is more effective at identifying negative cases compared to individual RBC indices. Implementation of the algorithm could efficiently reduce 10.0% (9/90) of the test volume of alpha globin gene analysis. A more stringent version of the algorithm that incorporates standard deviation in the cut-off values could potentially achieve nearly 100% sensitivity and reduce 5.6% (5/90) of the alpha globin gene analysis test volume.