Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed.MethodsTen CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.ResultsAn average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q < 0.05, fold change >2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value <0.05, minimum inclusion level difference >0.1).ConclusionThe RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis

Patellofemoral pain syndrome (PFPS): a systematic review of anatomy and potential risk factors

Patellofemoral Pain Syndrome (PFPS), a common cause of anterior knee pain, is successfully treated in over 2/3 of patients through rehabilitation protocols designed to reduce pain and return function to the individual. Applying preventive medicine strategies, the majority of cases of PFPS may be avoided if a pre-diagnosis can be made by clinician or certified athletic trainer testing the current researched potential risk factors during a Preparticipation Screening Evaluation (PPSE). We provide a detailed and comprehensive review of the soft tissue, arterial system, and innervation to the patellofemoral joint in order to supply the clinician with the knowledge required to assess the anatomy and make recommendations to patients identified as potentially at risk. The purpose of this article is to review knee anatomy and the literature regarding potential risk factors associated with patellofemoral pain syndrome and prehabilitation strategies. A comprehensive review of knee anatomy will present the relationships of arterial collateralization, innervations, and soft tissue alignment to the possible multifactoral mechanism involved in PFPS, while attempting to advocate future use of different treatments aimed at non-soft tissue causes of PFPS

Incidence and prevalence of patellofemoral pain: a systematic review and meta-analysis

Background: Patellofemoral pain is considered one of the most common forms of knee pain, affecting adults, adolescents, and physically active populations. Inconsistencies in reported incidence and prevalence exist and in relation to the allocation of healthcare and research funding, there is a clear need to accurately understand the epidemiology of patellofemoral pain. Methods: An electronic database search was conducted, as well as grey literature databases, from inception to June 2017. Two authors independently selected studies, extracted data and appraised methodological quality. If heterogeneous, data were analysed descriptively. Where studies were homogeneous, data were pooled through a meta-analysis. Results: 23 studies were included. Annual prevalence for patellofemoral pain in the general population was reported as 22.7%, and adolescents as 28.9%. Incidence rates in military recruits ranged from 9.7 – 571.4/1,000 person-years, amateur runners in the general population at 1080.5/1,000 person-years and adolescents amateur athletes 5.1% - 14.9% over 1 season. One study reported point prevalence within military populations as 13.5%. The pooled estimate for point prevalence in adolescents was 7.2% (95% Confidence Interval: 6.3% - 8.3%), and in female only adolescent athletes was 22.7% (95% Confidence Interval 17.4% - 28.0%). Conclusion: This review demonstrates high incidence and prevalence levels for patellofemoral pain. Within the context of this, and poor long term prognosis and high disability levels, PFP should be an urgent research priority

Dopamine D4 Receptor Gene Associated with Fairness Preference in Ultimatum Game

In experimental economics, the preference for reciprocal fairness has been observed in the controlled and incentivized laboratory setting of the ultimatum game, in which two individuals decide on how to divide a sum of money, with one proposing the share while the second deciding whether to accept. Should the proposal be accepted, the amount is divided accordingly. Otherwise, both would receive no money. A recent twin study has shown that fairness preference inferred from responder behavior is heritable, yet its neurogenetic basis remains unknown. The D4 receptor (DRD4) exon3 is a well-characterized functional polymorphism, which is known to be associated with attention deficit hyperactivity disorder and personality traits including novelty seeking and self-report altruism. Applying a neurogenetic approach, we find that DRD4 is significantly associated with fairness preference. Additionally, the interaction among this gene, season of birth, and gender is highly significant. This is the first result to link preference for reciprocal fairness to a specific gene and suggests that gene × environment interactions contribute to economic decision making

Research NoteThe proposed colonisation sequence of woody species in the Sourish Mixed Bushveld of the Limpopo province, South Africa

The long-term establishment sequence of the woody component of the Sourish Mixed Bushveld of the Limpopo province was studied and documented. Vegetation surveys were conducted at a protected site at the Towoomba Agricultural Development Centre during 1977 and 2000. Over the 23-year period, bush density at the site increased by 33%. Changes in the woody component indicated a shift from an acacia-dominated site to one dominated by broadleaved tree species. Early colonisers included mostly Acacia species (A. karroo, A. robusta, A. nilotica, A. gerrardii, A. tortilis, A. caffra, A. habeclada and A. mellifera), Dichrostachys cinerea and a few broadleaved species (Ximenia caffra, Dombeya rotundifolia and Searsia spp.). Intermediate colonisers included various shrubs (Diospyros lycioides, the Maytenus/Gymnosporia species group, Euclea species, Carissa bispinosa and Grewia spp.), a limited number of tree species (Pappea capensis, Boscia albitrunca and Ziziphus mucronata) and only two legumes (A. robusta and Peltophorum africanum). Late colonisers included only broadleaved shrubs and Waterberg Mountain Sourveld tree species (Grewia flavescens, Tarchonanthus camphoratus, Berchemia zeyerii, Cassine transvaalensis, Schotia brachypetala, Ximenia caffra, Heteropyxis natalensis, Terminalia sericea, Vangueria infausta and Searsia lancea). The leguminous and broadleaved components appeared to have distinct establishment sequences. Acacia spp. appeared to facilitate the early invasion of broadleaved woody species.African Journal of Range & Forage Science 2010, 27(2): 105–10

The short-term effect of fire on the woody component of the Sourish Mixed Bushveld

The short-term effect of an early-spring, moderately hot fire on the woody component of the Sourish Mixed Bushveld was monitored before, directly after, and for two successive seasons following the fire. The average height of trees less than three metres was reduced due to severe topkill, but trees higher than three metres were unaffected by the fire. Tree volume, leaf volume, total biomass and available browse initially decreased, but recovered within two seasons. Fire damage and regeneration depended on the structure of the woody component. Biomass production and woody seedling establishment was stimulated by the fire.Keywords: available browse; biomass; biomass production; browse; bush control; bushveld; damage; fire; mixed bushveld; regeneration; seedling establishment; sourish mixed bushveld; south africa; towoomba agricultural development centre; tree production; treesAfrican Journal of Range & Forage Science, 12(3): pp. 128-13

Toward a standardized investigation protocol in sudden unexpected deaths in infancy in South Africa: a multicenter study of medico-legal investigation procedures and outcomes.

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