Efficient CRISPR-mediated base editing in Agrobacterium spp.

Agrobacterium spp. are important plant pathogens that are the causative agents of crown gall or hairy root disease. Their unique infection strategy depends on the delivery of part of their DNA to plant cells. Thanks to this capacity, these phytopathogens became a powerful and indispensable tool for plant genetic engineering and agricultural biotechnology. Although Agrobacterium spp. are standard tools for plant molecular biologists, current laboratory strains have remained unchanged for decades and functional gene analysis of Agrobacterium has been hampered by time-consuming mutation strategies. Here, we developed clustered regularly interspaced short palindromic repeats (CRISPR)-mediated base editing to enable the efficient introduction of targeted point mutations into the genomes of both Agrobacterium tumefaciens and Agrobacterium rhizogenes As an example, we generated EHA105 strains with loss-of-function mutations in recA, which were fully functional for maize (Zea mays) transformation and confirmed the importance of RolB and RolC for hairy root development by A. rhizogenes K599. Our method is highly effective in 9 of 10 colonies after transformation, with edits in at least 80% of the cells. The genomes of EHA105 and K599 were resequenced, and genome-wide off-target analysis was applied to investigate the edited strains after curing of the base editor plasmid. The off-targets present were characteristic of Cas9-independent off-targeting and point to TC motifs as activity hotspots of the cytidine deaminase used. We anticipate that CRISPR-mediated base editing is the start of "engineering the engineer," leading to improved Agrobacterium strains for more efficient plant transformation and gene editing.

Oral health problems facing refugees in Europe: a scoping review.

INTRODUCTION: Europe has been experiencing a flow of refugees and asylum seekers driven by conflicts or poverty. Their oral health is often neglected despite its clear impact on quality of life. OBJECTIVE: To explore the status of oral health among refugees and asylum seekers groups by examining the available literature and to determine which evidence exists regarding the problems they face in terms of oral health. METHODS: The current paper followed PRISMA guidelines. A scoping review methodology was followed to retrieve 2911 records from five databases and grey literature. Twelve articles met the following inclusion criteria: experimental research concentrated on the oral and dental health of refugees and/or asylum seekers between 1995 and 2020 in English. Analysis was both descriptive and thematic, whilst a critical appraisal was applied using the Critical Appraisal Skills Program (CASP). RESULTS: Seven studies (58,3%) were quantitative, while five studies (41,6%) were qualitative. In general, the quality of most of the studies (83.3%) was good. Limited access to oral health care services was shown with a higher prevalence of oral diseases compared to the native populations of the host countries. Approaches to improve oral health have been implemented in some studies and have shown positive outcomes. CONCLUSIONS: Oral health care strategies should consider the oral health problems facing refugees in Europe, and oral health promotion campaigns are essential to give adequate guidance on how to access oral health care in the host countries.

A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.).

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

A Short-Read Genome Assembly Resource for Leveillula taurica Causing Powdery Mildew Disease of Sweet Pepper (Capsicum annuum).

Powdery mildew of sweet pepper (Capsicum annuum) is an economically important disease. It is caused by Leveillula taurica, an obligate biotrophic ascomycete with a partly endophytic mycelium and haustoria, i.e., feeding structures formed in the mesophyll cells of infected host plant tissues. The molecular basis of its pathogenesis is largely unknown because genomic resources only exist for epiphytically growing powdery mildew fungi with haustoria formed exclusively in epidermal cells of their plant hosts. Here, we present the first reference genome assembly for an isolate of L. taurica isolated from sweet pepper in Hungary. The short read-based assembly consists of 23,599 contigs with a total length of 187.2 Mbp; the scaffold N50 is 13,899 kbp and N90 is 3,522 kbp; and the average GC content is 39.2%. We detected at least 92,881 transposable elements covering 55.5 Mbp (30.4%). BRAKER predicted 19,751 protein-coding gene models in this assembly. Our reference genome assembly of L. taurica is the first resource to study the molecular pathogenesis and evolution of a powdery mildew fungus with a partly endophytic lifestyle.

Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana.

BACKGROUND: Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regulatory proteins and spliceosomal subunits. Although SR45 has orthologs in diverse eukaryotes, including human RNPS1, the sr45-1 null mutant is viable. Narrow flower petals and reduced seed formation suggest that SR45 regulates genes involved in diverse processes, including reproduction. To understand how SR45 is involved in the regulation of reproductive processes, we studied mRNA from the wild-type and sr45-1 inflorescences using RNA-seq, and identified SR45-bound RNAs by immunoprecipitation. RESULTS: Using a variety of bioinformatics tools, we identified a total of 358 SR45 differentially regulated (SDR) genes, 542 SR45-dependent alternative splicing (SAS) events, and 1812 SR45-associated RNAs (SARs). There is little overlap between SDR genes and SAS genes, and neither set of genes is enriched for flower or seed development. However, transcripts from reproductive process genes are significantly overrepresented in SARs. In exploring the fate of SARs, we found that a total of 81 SARs are subject to alternative splicing, while 14 of them are known Nonsense-Mediated Decay (NMD) targets. Motifs related to GGNGG are enriched both in SARs and near different types of SAS events, suggesting that SR45 recognizes this motif directly. Genes involved in plant defense are significantly over-represented among genes whose expression is suppressed by SR45, and sr45-1 plants do indeed show enhanced immunity. CONCLUSION: We find that SR45 is a suppressor of innate immunity. We find that a single motif (GGNGG) is highly enriched in both RNAs bound by SR45 and in sequences near SR45- dependent alternative splicing events in inflorescence tissue. We find that the alternative splicing events regulated by SR45 are enriched for this motif whether the effect of SR45 is activation or repression of the particular event. Thus, our data suggests that SR45 acts to control splice site choice in a way that defies simple categorization as an activator or repressor of splicing.

Assessment of the prevalence and risk factors of ophthalmoplegia among diabetic patients in a large national diabetes registry cohort.

BACKGROUND: There are limited data on the epidemiology and risk factors of ophthalmoplegia among diabetic patients. This study aims to determine the prevalence and important risk factors related to ophthalmoplegia among diabetic patients. METHODS: This is an observational registry-based study using the Saudi National Diabetes Registry (SNDR) database to select diabetic patients regardless of their diabetes type. A total of 64,351 Saudi diabetic patients aged more than 18 years and registered in SNDR between January 2000 and December 2010 were analyzed to identify ophthalmoplegic cases. Demographic, clinical, and biochemical parameters were studied and STROBE guidelines were used to design and report the results of this study. RESULTS: The overall prevalence of ophthalmoplegia cases was 0.32 %, further distributed into: 53.11 %, 36.36 %, and 2.8 % for cranial nerves VI, III, IV palsies respectively. Ophthalmoplegic cases were predominantly type 2 diabetic males with older age and longer diabetes duration. The most important and significant risk factors were age ≥ 45 years, diabetes duration ≥ 10 years, male gender and presence of retinopathy and nephropathy. CONCLUSIONS: Ophthalmoplegia is a rare entity associated mainly with type 2 diabetes. Clinicians have to consider its risk factors when screening or planning for prevention of this condition.

Dental and Periodontal Changes After Accelerated Correction of Lower Anterior Teeth Crowding With Periodontally Accelerated Osteogenic Orthodontics (PAOO) Procedure: A Randomized Controlled Trial.

Objective To evaluate the relative efficacy of periodontally accelerated osteogenic orthodontics (PAOO) compared to conventional fixed appliances in correcting lower anterior teeth crowding using a non-extraction treatment approach. Material and methods A single-center, two-arm, parallel-group randomized controlled trial was conducted on 38 patients (9 males, 29 females) with moderate crowding. These patients did not require premolar extraction and were randomly allocated into two treatment groups: the PAOO group and the conventional orthodontic treatment group. The Little Irregularity Index (LII) measured crowding intensity on pre-treatment study models. Changes in this index were recorded monthly in both treatment groups. The inter-canine width, inter-second-premolar width, plaque index (PI), gingival index (GI), and papillary bleeding index (PBI) were also measured before and after the leveling and alignment stage. Statistical analysis between the two groups was performed using Mann-Whitney U tests. Results For the LII, the average time for irregularity resolution was three months in the PAOO group, compared to five months in the conventional orthodontic treatment group. Regarding changes in inter-second-premolar width, the PAOO procedure led to a significant decrease in the increase of inter-second-premolar width, with an average increase of +1.52 mm compared to +2.71 mm in the control group. For the GI and PBI, it was found that their values significantly increased with PAOO application, averaging 0.18 and 0.17, respectively, compared to 0.05 and 0.07 in the control group. Conclusions The use of PAOO in orthodontic treatment accelerated the leveling and alignment process by 40%. Changes in the inter-canine width, the inter-second-premolar width, and the status of periodontal tissues were minimal and clinically negligible.

A Web-based interactive diabetes registry for health care management and planning in Saudi Arabia.

BACKGROUND: Worldwide, eHealth is a rapidly growing technology. It provides good quality health services at lower cost and increased availability. Diabetes has reached an epidemic stage in Saudi Arabia and has a medical and economic impact at a countrywide level. Data are greatly needed to better understand and plan to prevent and manage this medical problem. OBJECTIVE: The Saudi National Diabetes Registry (SNDR) is an electronic medical file supported by clinical, investigational, and management data. It functions as a monitoring tool for medical, social, and cultural bases for primary and secondary prevention programs. Economic impact, in the form of direct or indirect cost, is part of the registry's scope. The registry's geographic information system (GIS) produces a variety of maps for diabetes and associated diseases. In addition to availability and distribution of health facilities in the Kingdom, GIS data provide health planners with the necessary information to make informed decisions. The electronic data bank serves as a research tool to help researchers for both prospective and retrospective studies. METHODS: A Web-based interactive GIS system was designed to serve as an electronic medical file for diabetic patients retrieving data from medical files by trained registrars. Data was audited and cleaned before it was archived in the electronic filing system. It was then used to produce epidemiologic, economic, and geographic reports. A total of 84,942 patients were registered from 2000 to 2012, growing by 10% annually. RESULTS: The SNDR reporting system for epidemiology data gives better understanding of the disease pattern, types, and gender characteristics. Part of the reporting system is to assess quality of health care using different parameters, such as HbA1c, that gives an impression of good diabetes control for each institute. Economic reports give accurate cost estimation of different services given to diabetic patients, such as the annual insulin cost per patient for type 1, type 2, and gestational diabetes, which are 1155 SR (US $308), 1406 SR (US $375), and 1002 SR (US $267), respectively. Of this, 72.02% of the total insulin cost is spent on type 2 patients and 55.39% is in the form of premixed insulin. The SNDR can provide an accurate assessment of the services provided for research purposes. For example, only 27.00% of registered patients had an ophthalmic examination and only 71.10% of patients with proliferative retinopathy had laser therapy. CONCLUSIONS: The SNDR is an effective electronic medical file that can provide epidemiologic, economic, and geographic reports that can be used for disease management and health care planning. It is a useful tool for research and disease health care quality monitoring.

Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen.

BACKGROUND: The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In the absence of the otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating the activity of TEs and coding genes during the pathogenic life cycle. RESULTS: We performed time-course whole-transcriptome shotgun sequencing (RNA-seq) of total RNA derived from infected barley leaf epidermis at various stages of fungal pathogenesis and observed significant transcript accumulation and time point-dependent regulation of TEs in B. hordei. Using a manually curated consensus database of 344 TEs, we discovered phased small RNAs mapping to 104 consensus transposons, suggesting that RNA interference contributes significantly to their regulation. Further, we identified 5,127 long noncoding RNAs (lncRNAs) genome-wide in B. hordei, of which 823 originated from the antisense strand of a TE. Co-expression network analysis of lncRNAs, TEs, and coding genes throughout the asexual life cycle of B. hordei points at extensive positive and negative co-regulation of lncRNAs, subsets of TEs and coding genes. CONCLUSIONS: Our work suggests that similar to mammals and plants, fungal lncRNAs support the dynamic modulation of transcript levels, including TEs, during pivotal stages of host infection. The lncRNAs may support transcriptional diversity and plasticity amid loss of coding genes in powdery mildew fungi and may give rise to novel regulatory elements and virulence peptides, thus representing key drivers of rapid evolutionary adaptation to promote pathogenicity and overcome host defense.

Treatment effectiveness of young adults using clear aligners versus buccal fixed appliances in class I malocclusion with first premolar extraction using the ABO-Objective Grading System: A randomized controlled clinical trial.

OBJECTIVE: To compare the effectiveness of the clear aligners with the traditional fixed appliances in the treatment of premolars extraction complex cases using the American Board of Orthodontics Objective Grading System (ABO-OGS). MATERIAL AND METHODS: A single-centre, 2-parallel groups RCT with two arms. Forty severe crowding patients (14 males, 26 females; mean age: 21.40±2.42) who required four first premolars extraction were included and randomly allocated into two treatment groups: clear aligners therapy group (CAT), and fixed appliances therapy group (FAT). Cases complexities were measured on pre-treatment records using the Discrepancy index (DI). Post-treatment records were evaluated using the American Board of Orthodontics Objective Grading System (ABO-OGS). Two sample t-tests and Fisher's Exact tests were used to test for significant differences between the two groups. The statistical significance was set at P < 0.006 using Bonferroni's correction. RESULTS: For the DI, the mean scores were 32.25 (± 4.33) in the CAT group and 33 (± 7.92) in the FAT group. In the CAT group, the total OGS score ranged between 6-33 points with an average of 17.50(± 7.41), whereas the total score in the FAT group went between 4-30 points with an average of 12.89 (± 6.31) with no significant differences between the two groups (P=0.05). When comparison of the successful cases between the two groups was made, 11 cases received passing scores, and 9 cases received failing scores in the CAT group. Whereas in the FAT group, 17 cases received passing scores, and 3 received a failing score. No statistically significant differences were found in the passing rates between of the CAT and FAT groups (P = 0.421). CONCLUSIONS: According to the ABO-OGS total scores, there was no significant difference between the clear aligners and fixed appliances in the treatment of class I severe crowding cases with first premolars extraction in young adults. There were no differences between the two techniques in the OGS components scores except for the occlusal contacts, which were significantly better with the fixed appliances. When comparing the number of successful and failed cases between the two groups, no significant differences were noted, with the fixed appliances having a 30% higher success rate than the clear aligners, which must be considered clinically when choosing between these two techniques in the complex orthodontic cases treatment.

Assessment of Dentoalveolar Changes Following Leveling and Alignment of Severely Crowded Upper Anterior Teeth Using Self-Ligating Brackets Alone or With Flapless Piezocision Compared to Traditional Brackets: A Randomized Controlled Clinical Trial.

Introduction Dental crowding is one of the most common types of malocclusions. It can be treated with or without extraction, depending on the severity of the crowding. Extraction-based orthodontic treatments are the preferred treatment option in cases of severe crowding, but they take longer than non-extraction cases. Objective This study aimed to evaluate the dentoalveolar changes following the orthodontic treatment of severely crowded maxillary anterior teeth in adults using self-ligating brackets alone or combined with flapless piezocision. Materials and methods The participants in this study were 63 patients (46 females and 17 males; mean age SD: 19.71 ± 2.74 years) who attended the Department of Orthodontics at the University of Damascus from January 2020 to December 2021. The participants were divided into three groups at random: Group (1): traditional brackets group, Group (2): self-ligating brackets group; and Group (3): self-ligating brackets with flapless piezocision group. Little's Irregularity Index (LII) was measured at five assessment times: before the onset of orthodontic treatment (T0), after one month (T1), after two months (T2), after three months (T3), and at the end of the leveling and alignment phase (T4). The intercanine width (lingual), the intercanine width (cusp), and the canine rotation angle were measured at two assessment times: before the onset of orthodontic treatment (T0) and at the end of the leveling and alignment phase (T4). Results The three studied groups had statistically significant differences in terms of LII during the first three months, and the most significant improvement of LII was in the self-ligating brackets with the piezocision group (P < 0.001). In addition, the intercanine width (cusp) at the end of the leveling and aligning phase revealed greater mean values in both self-ligating brackets groups compared to the traditional brackets group, and the differences were statistically significant (P < 0.001). Otherwise, no statistically significant differences were found at the end of the leveling and aligning phase in the intercanine width (lingual) or the canine rotation angle between the three studied groups (P > 0.05). Conclusion Using self-ligating brackets with flapless piezocision revealed more significant results concerning LII as compared to other groups. Thus, combining these two acceleration methods could get more effective results in aligning severely crowded teeth. Self-ligating brackets, whether used alone or with flapless piezocision, resulted in greater intercanine width at the cusp level. The type of brackets (traditional or self-ligating) did not affect the canine rotation angle.

Leveling and alignment time and the periodontal status in patients with severe upper crowding treated by corticotomy-assisted self-ligating brackets in comparison with conventional or self-ligating brackets only: a 3-arm randomized controlled clinical trial.

INTRODUCTION: The lengthy period of time required is one of the main reasons patients refuse orthodontic treatment. In addition, treatment may have negative effects on periodontal tissues. OBJECTIVE: This study aimed to evaluate the overall time needed for leveling and alignment and the periodontal indices in adult patients with severe crowding. Patients were treated using either self-ligating brackets associated with flapless corticotomy (SLBs + FC group), self-ligating brackets alone (SLBs group), or conventional brackets (CBs group) alone. MATERIALS AND METHODS: A total of 57 adult patients (10 male patients, 47 female patients) referred to the Department of Orthodontics, the University of Damascus Dental School from August 2018 to March 2019, were enrolled in this trial. The patients were randomly allocated to 1 of 3 groups: CBs (mean age: 19.62 ± 2.42 years), SLBs (mean age: 19.98 ± 2.84 years), or SLBs + FC (mean age: 20.67 ± 2.59 years). The overall alignment time for the upper anterior teeth was calculated. The following periodontal parameters were measured at 5 assessment times: plaque index, gingival index, papillary bleeding index, and probing depth. RESULTS: The average leveling and alignment time was 81.89 ± 9.49 days, 123 ± 10.69 days, and 165.25 ± 13.05 days for the SLBs + FC group, the SLBs group, and the CBs group, respectively. A significant reduction in the overall alignment duration was found in the SLBs + FC group by 50%, and in the SLBs group by 25%, compared to the control group, with a statistically significant difference among the 3 groups (P < 0.001). There were statistically significant differences in the periodontal indices (except probing depth) after 1 month, with values greater in the SLBs + FC group (P < 0.05). CONCLUSIONS: Using self-ligating brackets in combination with flapless corticotomy may be effective in accelerating upper dental decrowding in adult patients, with a reduction of 50% of the normal treatment time using traditional brackets. Using self-ligating brackets alone reduced treatment time by 25%. The adjunctive flapless corticotomy did not cause clinically negative effects on the periodontal tissues.

Evaluation of Patient-Centered Outcomes Associated With the Acceleration of Upper Incisor Decrowding Using Self-Ligating Brackets With or Without Piezocision in Comparison With Traditional Brackets: A Three-Arm Randomized Controlled Trial.

Introduction The pain and discomfort associated with orthodontic treatment are considered undesirable complications which may negatively affect the patient's cooperation and reduce the efficiency of orthodontic treatment. This trial aimed to assess patient-centered outcomes in the treatment of class I malocclusion with severe crowding using self-ligating brackets (SLBs) with or without an acceleration procedure (piezocision) compared to the traditional brackets (TBs) in a three-arm trial. Materials and Methods Sixty-six patients (51 females, 15 males; mean age ± SD: 20.08 ± 2.61 years) attending the Department of Orthodontics, the University of Damascus, Damascus (Syria) from April 2019 to October 2020 participated in this study. The patients were randomly allocated to three groups: the TBs s group (n = 22; mean age ± SD: 18.72 ± 2.42), the SLBs group (n = 22; mean age ± SD: 20.48 ± 2.84), and the SLBs with the piezocision group (SLBs+P; n = 22; mean age ± SD: 19.17 ± 2.59). Patient-centered outcomes were assessed using two standardized questionnaires depending on visual analog scales (VAS) for the majority of the questions and a binary scale (Yes/No) for the last two questions in the second questionnaire. The levels of pain, discomfort, swelling, difficulties with mastication, swallowing, and jaw movement restriction were measured at five assessment times: one day (T1), 3 days (T2), 7 days (T3), 14 days (T4), and 28 days (T5) after the beginning of treatment. The satisfaction levels, acceptance to undergo the applied treatment again, and willingness to advise a friend to receive similar treatment were measured at the last assessment time (T5). One-way ANOVA test or its alternative nonparametric test (i.e., Kruskal-Wallis test) was utilized to compare the three groups. Results There were statistically significant differences between the three groups regarding pain, discomfort, swelling, difficulties with mastication, problems with swallowing, and jaw movement restriction during the first three assessment times only (T1, T2, and T3; P < 0.001). The differences were mainly between the SLBs+P group and the other two groups, where the mean values were greater in the SLBs+P group. Otherwise, there were no significant statistical differences between the SLBs and the TBs groups. Concerning patients' satisfaction with the provided treatment, a statistically significant difference between the three groups was detected after 28 days (T5; P < 0.001). The SLBs+P group showed the lowest mean values, whereas there were no significant differences between the two other groups. Conclusion The levels of pain and discomfort, swelling, difficulties in mastication and swallowing, and restriction of jaw movement were greater in SLBs with the piezocision group compared to the sole use of SLBs or TBs in the first week only. The patients showed a high level of satisfaction with the applied therapeutic procedures, which means that SLBs alone or in combination with piezocision can be an accepted treatment modality by patients in the acceleration of orthodontic tooth movement.

Assessment of Patient-Centered Outcomes When Treating Maxillary Constriction Using a Slow Removable Versus a Rapid Fixed Expansion Appliance in the Adolescence Period: A Randomized Controlled Trial.

Objective This study aimed to evaluate and compare the levels of pain, discomfort, and functional impairments between slow and rapid maxillary expansion (RME) in treating skeletal maxillary constriction in the adolescence period (i.e., between 12 and 16 years). Materials and methods The study sample consisted of 52 patients (21 males and 31 females) with maxillary skeletal constriction in the posterior region. The patients were randomly distributed into either RME (26 patients, with a mean age of 13.87 (± 1.31) years) or slow maxillary expansion group (SME, 26 patients, with a mean age of 14.31 (± 1.19) years). The levels of pain, discomfort, and functional difficulties were assessed after 24 hours (T1), 7 days (T2), 15 days (T3), one month (T4), and four months (T5) following the onset of the expansion procedure. Results Patients in the RME group encountered significantly greater levels of pain and discomfort than those in the SME group at T1, T2, and T3 (p>0.001). Chewing and swallowing difficulties were significantly greater in the RME group at T1, T2, T3, and T4 (P≤0.001). The pressure on soft tissue was greater in the RME group at T2 and T3 (p>0.001). After four months (T5), the levels of pain and discomfort decreased to their lowest levels, as well as the difficulties of chewing and swallowing, and the pressure on soft tissue were almost non-existent in both groups. Conclusion Patients treated with the removable slow maxillary expander reported lower levels of pain and discomfort, fewer chewing and swallowing difficulties, and less pressure on soft tissues than those treated with the bonded rapid maxillary expander. These difficulties gradually decreased over time in both groups. The lower levels of pain and discomfort may make the SME an effective and comfortable treatment alternative for adolescents with skeletal maxillary constriction.

Transcriptional response to host chemical cues underpins the expansion of host range in a fungal plant pathogen lineage.

The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic. The fungus Sclerotinia sclerotiorum has been reported to parasitize more than 400 plant species from diverse eudicot families while its close relative, S. trifoliorum, is restricted to plants from the Fabaceae family. We analyzed S. sclerotiorum global transcriptome reprogramming on hosts from six botanical families and reveal a flexible, host-specific transcriptional program. We generated a chromosome-level genome assembly for S. trifoliorum and found near-complete gene space conservation in two representative strains of broad and narrow host range Sclerotinia species. However, S. trifoliorum showed increased sensitivity to the Brassicaceae defense compound camalexin. Comparative analyses revealed a lack of transcriptional response to camalexin in the S. trifoliorum strain and suggest that regulatory variation in detoxification and effector genes at the population level may associate with the genetic accommodation of Brassicaceae in the Sclerotinia host range. Our work proposes transcriptional plasticity and the co-existence of signatures for generalist and polyspecialist adaptive strategies in the genome of a plant pathogen.

The Efficacy of Accelerating Orthodontic Tooth Movement by Combining Self-Ligating Brackets With One or More Acceleration Methods: A Systematic Review.

This review aimed to evaluate the effectiveness of using one or more acceleration methods with self-ligating brackets to accelerate orthodontic tooth movement in adults and the associated effects of these interventions. An electronic search of the following databases (PubMed, Scopus, Google Scholar, EMBASE) was performed (From January 1990 to November 2021). ClinicalTrials.gov and the International Clinical Trials Registry Platform were also electronically searched to find any unpublished studies and ongoing trials. The selected randomized controlled trials (RCTs) involved adult patients treated using self-ligating brackets combined with one or more acceleration methods compared with self-ligating brackets or conditional brackets alone. The risk of bias was assessed using Cochrane's risk of bias tool. A total of seven RCTs and one controlled clinical trial (CCT) were included in this review. Combining self-ligating brackets with flapless corticotomy, low-level laser therapy (LLLT), and infrared light accelerated orthodontic movement by 43% and 50% for surgical methods, 20-50% for LLLT, and 22% for infrared light. Regarding side effects on periodontal tissues, neither flapless corticotomy nor low-frequency vibrational forces caused any damage. Combining self-ligating brackets and flapless corticotomy, low-level laser, or infrared light effectively accelerated orthodontic movement by 20% to 50 %. In contrast, the combination of self-ligating brackets with vibrational forces did not affect speeding tooth movement. The acceleration methods did not have any side effects on the periodontal tissues, but the available evidence was insufficient. There is a need for further primary research regarding the effectiveness of combining self-ligating brackets with acceleration methods and the possible untoward side effects.

Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways.

BACKGROUND: Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plant cells. The expression of some plant genes is altered by the nematode as it establishes its feeding site. RESULTS: We examined the expression of soybean (Glycine max) genes in galls formed in roots by the root-knot nematode, Meloidogyne incognita, 12 days and 10 weeks after infection to understand the effects of infection of roots by M. incognita. Gene expression was monitored using the Affymetrix Soybean GeneChip containing 37,500 G. max probe sets. Gene expression patterns were integrated with biochemical pathways from the Kyoto Encyclopedia of Genes and Genomes using PAICE software. Genes encoding enzymes involved in carbohydrate and cell wall metabolism, cell cycle control and plant defense were altered. CONCLUSIONS: A number of different soybean genes were identified that were differentially expressed which provided insights into the interaction between M. incognita and soybean and into the formation and maintenance of giant cells. Some of these genes may be candidates for broadening plants resistance to root-knot nematode through over-expression or silencing and require further examination.

Post-transcriptional gene silencing of root-knot nematode in transformed soybean roots.

RNAi constructs targeted to four different genes were examined to determine their efficacy to reduce galls formed by Meloidogyne incognita in soybean roots. These genes have high similarity with essential soybean cyst nematode (Heterodera glycines) and Caenorhabditis elegans genes. Transformed roots were challenged with M. incognita. Two constructs, targeted to genes encoding tyrosine phosphatase (TP) and mitochondrial stress-70 protein precursor (MSP), respectively, strongly interfered with M. incognita gall formation. The number of galls formed on roots transformed with constructs targeting the M. incognita TP and MSP genes was reduced by 92% and 94.7%, respectively. The diameter of M. incognita inside these transformed roots was 5.4 and 6.5 times less than the diameter of M. incognita found inside control plants transformed with the empty vector. These results indicate that silencing the genes encoding TP and MSP can greatly decrease gall formation and shows a promising solution for broadening resistance of plants against this plant-parasitic nematode.

Pathogen Effectors: Exploiting the Promiscuity of Plant Signaling Hubs.

Pathogens produce effectors to overcome plant immunity, thereby threatening crop yields and global food security. Large-scale interactomic studies have revealed that pathogens from different kingdoms of life target common plant proteins during infection, the so-called effector hubs. These hubs often play central roles in numerous plant processes through their ability to interact with multiple plant proteins. This ability arises partly from the presence of intrinsically disordered domains (IDDs) in their structure. Here, we highlight the role of the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) and JASMONATE-ZIM DOMAIN (JAZ) transcription regulator families as plant signaling and effector hubs. We consider different evolutionary hypotheses to rationalize the existence of diverse effectors sharing common targets and the possible role of IDDs in this interaction.

Genome-wide alternative splicing profiling in the fungal plant pathogen Sclerotinia sclerotiorum during the colonization of diverse host families.

Sclerotinia sclerotiorum is a notorious generalist plant pathogen that threatens more than 600 host plants, including wild and cultivated species. The molecular bases underlying the broad compatibility of S. sclerotiorum with its hosts is not fully elucidated. In contrast to higher plants and animals, alternative splicing (AS) is not well studied in plant-pathogenic fungi. AS is a common regulated cellular process that increases cell protein and RNA diversity. In this study, we annotated spliceosome genes in the genome of S. sclerotiorum and characterized their expression in vitro and during the colonization of six host species. Several spliceosome genes were differentially expressed in planta, suggesting that AS was altered during infection. Using stringent parameters, we identified 1,487 S. sclerotiorum genes differentially expressed in planta and exhibiting alternative transcripts. The most common AS events during the colonization of all plants were retained introns and the alternative 3' receiver site. We identified S. sclerotiorum genes expressed in planta for which (a) the relative accumulation of alternative transcripts varies according to the host being colonized and (b) alternative transcripts harbour distinct protein domains. This notably included 42 genes encoding predicted secreted proteins showing high-confidence AS events. This study indicates that AS events are taking place in the plant pathogenic fungus S. sclerotiorum during the colonization of host plants and could generate functional diversity in the repertoire of proteins secreted by S. sclerotiorum during infection.