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Pathogenic variants in the transcription factor TP63 are associated with clinically overlapping syndromes including ectrodactyly-ectodermal dysplasia clefting (EEC) and ankyloblepharon-ectodermal defects-cleft lip/palate (AEC). T cell lymphopenia has rarely been described in individuals with TP63 variants and the cause of the T cell defect is unclear. Here, we present a case of a female infant born with TP63-related syndrome and profound T cell lymphopenia, first uncovered through newborn screening. Flow cytometry analysis revealed low CD4+ naïve T cells and nearly absent CD8+ T cells with intact B and NK cell compartments. A de novo heterozygous pathogenic variant c.1040 G>A (C347Y) in exon 8 of TP63 was identified. An artificial thymic organoid system, to assess the intrinsic ability of the patient’s hematopoietic cells to develop into T cells, was performed twice using separate peripheral blood samples. Ex vivo T cell differentiation was evident with the artificial organoid system, suggesting that a thymic stromal cell defect may be the cause of the T cell lymphopenia. Consistent with this, interrogation of publicly available data indicated that TP63 expression in the human thymus is restricted to thymic epithelial cells. Based on these data, congenital athymia was suspected and the patient received an allogenic cultured thymus tissue implant (CTTI). This is the first report of suspected congenital athymia and attempted treatment with CTTI associated with TP63 variant. At 9 months post-implant, peripheral lymphocyte analysis revealed measurable T cell receptor excision circles and presence of CD4+ recent thymic emigrants suggestive of early thymopoiesis. She will continue regular monitoring to ensure restoration of T cell immunity.

Abstract Background Sub‐classification of hidradenitis suppurativa (HS) may allow for a better understanding of disease aetiology and disease burden, and eventually permit a more personalised treatment for patients. Objective To identify patient subtypes of HS based on comorbidity patterns and clinical characteristics, and to examine their inflammatory and metabolic blood profiles and associated levels of experienced distress, pain, quality of life, employment status and prescribed treatments. Methods Cluster analysis of clinical data from consecutive, newly referred adult HS patients attending a dermatological hospital department. Results A total of 534 patients (338 women and 196 men) with a mean age of 40.5 years (SD = 13.7) were included; 35.4% had Hurley stage I, 50.4% had Hurley stage II, and 14.8% had Hurley stage III. In total, six disease subtypes were identified: ‘female subtype’ (n = 182, 34.1%), ‘familial subtype’ (n = 144, 27.0%), ‘diabetes subtype’ (n = 107, 20.0%), ‘psychiatric disease subtype’ (n = 49, 9.2%), ‘Crohn's disease subtype’ (n = 29, 5.4%) and ‘asthma subtype’ (n = 23, 4.3%). Patients with ‘Crohn's disease subtype’ and ‘diabetes subtype’ had highest levels of systemic inflammation (C‐reactive protein, erythrocyte sedimentation rate, leucocytes and neutrophils), blood glucose and lipids (triglycerides), p

AimsPelvic discontinuity is a rare but increasingly common complication of total hip arthroplasty (THA). This single-centre study evaluated the performance of custom-made triflange acetabular components in acetabular reconstruction with pelvic discontinuity by determining: 1) revision and overall implant survival rates; 2) discontinuity healing rate; and 3) Harris Hip Score (HHS).MethodsRetrospectively collected data of 38 patients (39 hips) with pelvic discontinuity treated with revision THA using a custom-made triflange acetabular component were analyzed. Minimum follow-up was two years (mean 5.1 years (2 to 11)).ResultsThere were eight subsequent surgical interventions. Two failures (5%) of the triflange acetabular components were both revised because of deep infection. There were seven (18%) patients with dislocation, and five (13%) of these were treated with a constraint liner. One patient had a debridement, antibiotics, and implant retention (DAIR) procedure. In 34 (92%) hips the custom-made triflange component was considered stable, with a healed pelvic discontinuity with no aseptic loosening at midterm follow-up. Mean HHS was 80.5 (48 to 96).ConclusionThe performance of the custom triflange implant in this study is encouraging, with high rates of discontinuity healing and osteointegration of the acetabular implant with no aseptic loosening at midterm follow-up. However, complications are not uncommon, particularly instability which we successfully addressed with constrained liners.Cite this article: Bone Jt Open 2022;3(11):867–876.

The thymus, a primary lymphoid organ, produces the T cells of the immune system. Originating from the 3rd pharyngeal pouch during embryogenesis, this organ functions throughout life. Yet, thymopoiesis can be transiently or permanently damaged contingent on the types of systemic stresses encountered. The thymus also undergoes a functional decline during aging, resulting in a progressive reduction in naïve T cell output. This atrophy is evidenced by a deteriorating thymic microenvironment, including, but not limited, epithelial-to-mesenchymal transitions, fibrosis and adipogenesis. An exploration of cellular changes in the thymus at various stages of life, including mouse models of in-born errors of immunity and with single cell RNA sequencing, is revealing an expanding number of distinct cell types influencing thymus functions. The thymus microenvironment, established through interactions between immature and mature thymocytes with thymus epithelial cells (TEC), is well known. Less well appreciated are the contributions of neural crest cell-derived mesenchymal cells, endothelial cells, diverse hematopoietic cell populations, adipocytes, and fibroblasts in the thymic microenvironment. In the current review, we will explore the contributions of the many stromal cell types participating in the formation, expansion, and contraction of the thymus under normal and pathophysiological processes. Such information will better inform approaches for restoring thymus functionality, including thymus organoid technologies, beneficial when an individuals’ own tissue is congenitally, clinically, or accidentally rendered non-functional.

The implementation of next-generation sequencing (NGS) in clinical oncology has enabled the analysis of multiple cancer-associated genes for diagnostics and treatment purposes. The detection of pathogenic and likely pathogenic mutations is crucial to manage the disease. Obtaining the mutational profile may be challenging in samples with low yields of DNA—reflected by the type of biological material, such as formalin-fixed paraffin-embedded tissue (FFPE), needle biopsies, and circulating free/tumor DNA, as well as a sparse tumor content. Moreover, standardized strict procedures for the extraction of DNA in a clinical setting might contribute to lower amounts of DNA per µL. The detection of variants in low-yield DNA samples remains a challenge in clinical diagnostics, where molecular analyses such as NGS are needed. Here, we performed vacuum centrifugation on DNA extracted from five FFPE tissue blocks, with concentrations below 0.2 ng/µL. Through NGS analysis, we found that low-yield DNA samples could be concentrated to sufficient levels, without compromising the mutational profile.

Nearly one third of the world’s population is infected with Mycobacterium tuberculosis (Mtb). While much work has focused on the role of different Mtb encoded proteins in pathogenesis, recent studies have revealed that Mtb also transcribes many noncoding RNAs whose functions remain poorly characterized. We performed RNA sequencing and identified a subset of Mtb H37Rv-encoded small RNAs (

22q11.2 deletion syndrome (DiGeorge), CHARGE syndrome, Nude/SCID and otofaciocervical syndrome type 2 (OTFCS2) are distinct clinical conditions in humans that can result in hypoplasia and occasionally, aplasia of the thymus. Thymic hypoplasia/aplasia is first suggested by absence or significantly reduced numbers of recent thymic emigrants, revealed in standard-of-care newborn screens for T cell receptor excision circles (TRECs). Subsequent clinical assessments will often indicate whether genetic mutations are causal to the low T cell output from the thymus. However, the molecular mechanisms leading to the thymic hypoplasia/aplasia in diverse human syndromes are not fully understood, partly because the problems of the thymus originate during embryogenesis. Rodent and Zebrafish models of these clinical syndromes have been used to better define the underlying basis of the clinical presentations. Results from these animal models are uncovering contributions of different cell types in the specification, differentiation, and expansion of the thymus. Cell populations such as epithelial cells, mesenchymal cells, endothelial cells, and thymocytes are variably affected depending on the human syndrome responsible for the thymic hypoplasia. In the current review, findings from the diverse animal models will be described in relation to the clinical phenotypes. Importantly, these results are suggesting new strategies for regenerating thymic tissue in patients with distinct congenital disorders.

Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploinsufficiency of ~106 genes, which comprise coding RNAs, noncoding RNAs, and pseudogenes. The consequent haploinsufficiency of many of the coding genes are well described, including the key roles of T-box Transcription Factor 1 (TBX1) and DiGeorge Critical Region 8 (DGCR8) in the clinical phenotypes. However, the haploinsufficiency of these genes alone cannot account for the tremendous variation in the severity and penetrance of the clinical complications among those affected. Recent RNA and DNA sequencing approaches are uncovering novel genetic and epigenetic differences among 22q11.2del patients that can influence disease severity. In this review, the role of coding and non-coding genes, including microRNAs (miRNA) and long noncoding RNAs (lncRNAs), will be discussed in relation to their bearing on 22q11.2del with an emphasis on TBX1.

Israel is a country in the Near East consisting for 95% of the arid regions in which 60% of the territory are covered by the Negev Desert. Therefore, the water resources are scant here and formed mostly by atmospheric precipitations. In the period from 1989 to 2005 the average precipitations were 6 billion cu. m, of which 60–70% were evaporated soon after rainfalls, at least 5% run down by rivers into the sea (mostly in winter) and the remaining 25% of precipitations infiltrated into soil from where the greater part of water got into the sea with ground waters. In Israel there are two groups of water resources: surface and underground. Israel is not rich in surface waters. The natural reservoir of surface fresh water is the Kinneret Lake in the northeast of the country. It gets water from the Jordan River and its tributaries. The average annual amount of available water of this lake is around 370 million cu. m, which accounts for one-third of the country’s water needs and still higher share of the drinking water needs. The greater part of fresh waters (37% of water supply of Israel as of 2011) in this country is supplied from ground water sources. Owing to insufficiency of available natural resources, unevenness of precipitations by years and seasons and with the growth of the population and economic development the issues of provision with the quality drinking water of the population as well as agriculture and industry, rehabilitation of natural environment cause permanently growing concern. In view of the water shortage untiring efforts have been taken to improve the irrigation efficiency and to reduce water use by improving the efficacy of irrigation techniques and application of advanced system management approaches. Among the water saving technologies applied in Israel there are: drop irrigation, advanced filtration, up to date methods of water leak detection from networks, rainwater collection and processing systems. At the same time such measures as water flow measurements, policy of water price formation, changeover to cultivation of valuable crops, thermal water recycling, computer-based and remotely controlled irrigation are also applied. The search for new techniques of fresh water production is going on. Water saving is considered the most reliable and less costly method to increase water resources of the country, And this task is being accomplished in all sectors. In 1964 the National Water Carrier of Israel was constructed. The main task of this project is to achieve the reliable compensation of the difference between water income in various regions (north and south), in different seasons (summer and winter) and in different years (with sufficient and insufficient precipitations). In 1999 the Israel government initiated the long-term large-scale program of sea water desalination for production of drinking water for internal use. Reverse osmosis was adopted the basic technique for desalination of brackish and sea water. Currently there are five sea water desalination plants producing about 600 million cu. m of desalinated water per year which is equivalent to approximately 42% of the country’s drinking water needs. Israel adopted the General Plan of Water Economy Development for 2010–2050, which envisages complete coverage of water deficit by way of entire wastewater treatment and construction of additional sea water desalination facilities with a capacity to 1500 million cu. m by 2050. Any additional desalinated water that may become available in these years will be used for replenishing the water supply in Israel.

This review is a part of the SI ‘Genome-Scale Modeling of Microorganisms in the Real World’. The goal of GEM is the accurate prediction of the phenotype from its respective genotype under specified environmental conditions. This review focuses on the dynamic phenotype; prediction of the real-life behaviors of microorganisms, such as cell proliferation, dormancy, and mortality; balanced and unbalanced growth; steady-state and transient processes; primary and secondary metabolism; stress responses; etc. Constraint-based metabolic reconstructions were successfully started two decades ago as FBA, followed by more advanced models, but this review starts from the earlier nongenomic predecessors to show that some GEMs inherited the outdated biokinetic frameworks compromising their performances. The most essential deficiencies are: (i) an inadequate account of environmental conditions, such as various degrees of nutrients limitation and other factors shaping phenotypes; (ii) a failure to simulate the adaptive changes of MMCC (MacroMolecular Cell Composition) in response to the fluctuating environment; (iii) the misinterpretation of the SGR (Specific Growth Rate) as either a fixed constant parameter of the model or independent factor affecting the conditional expression of macromolecules; (iv) neglecting stress resistance as an important objective function; and (v) inefficient experimental verification of GEM against simple growth (constant MMCC and SGR) data. Finally, we propose several ways to improve GEMs, such as replacing the outdated Monod equation with the SCM (Synthetic Chemostat Model) that establishes the quantitative relationships between primary and secondary metabolism, growth rate and stress resistance, process kinetics, and cell composition.

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), with 10.4 million new cases per year reported in the human population. Recent studies on the Mtb transcriptome have revealed the abundance of noncoding RNAs expressed at various phases of mycobacteria growth, in culture, in infected mammalian cells, and in patients. Among these noncoding RNAs are both small RNAs (sRNAs) between 50 and 350 nts in length and smaller RNAs (sncRNA) < 50 nts. In this review, we provide an up-to-date synopsis of the identification, designation, and function of these Mtb-encoded sRNAs and sncRNAs. The methodological advances including RNA sequencing strategies, small RNA antagonists, and locked nucleic acid sequence-specific RNA probes advancing the studies on these small RNA are described. Initial insights into the regulation of the small RNA expression and putative processing enzymes required for their synthesis and function are discussed. There are many open questions remaining about the biological and pathogenic roles of these small non-coding RNAs, and potential research directions needed to define the role of these mycobacterial noncoding RNAs are summarized.

Lee et al [...]

ABSTRACT Haemophilus ducreyi causes chancroid, a sexually transmitted infection. A primary means by which this pathogen causes disease involves eluding phagocytosis; however, the molecular basis for this escape mechanism has been poorly understood. Here, we report that the LspA virulence factors of H. ducreyi inhibit phagocytosis by stimulating the catalytic activity of C-terminal Src kinase (Csk), which itself inhibits Src family protein tyrosine kinases (SFKs) that promote phagocytosis. Inhibitory activity could be localized to a 37-kDa domain (designated YL2) of the 456-kDa LspA1 protein. The YL2 domain impaired ingestion of IgG-opsonized targets and decreased levels of active SFKs when expressed in mammalian cells. YL2 contains tyrosine residues in two EPIYG motifs that are phosphorylated in mammalian cells. These tyrosine residues were essential for YL2-based inhibition of phagocytosis. Csk was identified as the predominant mammalian protein interacting with YL2, and a dominant-negative Csk rescued phagocytosis in the presence of YL2. Purified Csk phosphorylated the tyrosines in the YL2 EPIYG motifs. Phosphorylated YL2 increased Csk catalytic activity, resulting in positive feedback, such that YL2 can be phosphorylated by the same kinase that it activates. Finally, we found that the Helicobacter pylori CagA protein also inhibited phagocytosis in a Csk-dependent manner, raising the possibility that this may be a general mechanism among diverse bacteria. Harnessing Csk to subvert the Fcγ receptor (FcγR)-mediated phagocytic pathway represents a new bacterial mechanism for circumventing a crucial component of the innate immune response and may potentially affect other SFK-involved cellular pathways. IMPORTANCE Phagocytosis is a critical component of the immune system that enables pathogens to be contained and cleared. A number of bacterial pathogens have developed specific strategies to either physically evade phagocytosis or block the intracellular signaling required for phagocytic activity. Haemophilus ducreyi, a sexually transmitted pathogen, secretes a 4,153-amino-acid (aa) protein (LspA1) that effectively inhibits FcγR-mediated phagocytic activity. In this study, we show that a 294-aa domain within this bacterial protein binds to C-terminal Src kinase (Csk) and stimulates its catalytic activity, resulting in a significant attenuation of Src kinase activity and consequent inhibition of phagocytosis. The ability to inhibit phagocytosis via Csk is not unique to H. ducreyi, because we found that the Helicobacter pylori CagA protein also inhibits phagocytosis in a Csk-dependent manner. Harnessing Csk to subvert the FcγR-mediated phagocytic pathway represents a new bacterial effector mechanism for circumventing the innate immune response.

We report a skew-Laplace statistical analysis of both flow cytometry scatters and cell size from microbial strains primarily grown in batch cultures, others in chemostat cultures and bacterial aquatic populations. Cytometry scatters best fit the skew-Laplace distribution while cell size as assessed by an electronic particle analyzer exhibited a moderate fitting. Unlike the cultures, the aquatic bacterial communities clearly do not fit to a skew-Laplace distribution. Due to its versatile nature, the skew-Laplace distribution approach offers an easy, efficient, and powerful tool for distribution of frequency analysis in tandem with the flow cytometric cell sorting.

Pathogenic variants in the transcription factor TP63 are associated with clinically overlapping syndromes including ectrodactyly-ectodermal dysplasia clefting (EEC) and ankyloblepharon-ectodermal defects-cleft lip/palate (AEC). T cell lymphopenia has rarely been described in individuals with TP63 variants and the cause of the T cell defect is unclear. Here, we present a case of a female infant born with TP63-related syndrome and profound T cell lymphopenia, first uncovered through newborn screening. Flow cytometry analysis revealed low CD4+ naïve T cells and nearly absent CD8+ T cells with intact B and NK cell compartments. A de novo heterozygous pathogenic variant c.1040 G>A (C347Y) in exon 8 of TP63 was identified. An artificial thymic organoid system, to assess the intrinsic ability of the patient's hematopoietic cells to develop into T cells, was performed twice using separate peripheral blood samples. Ex vivo T cell differentiation was evident with the artificial organoid system, suggesting that a thymic stromal cell defect may be the cause of the T cell lymphopenia. Consistent with this, interrogation of publicly available data indicated that TP63 expression in the human thymus is restricted to thymic epithelial cells. Based on these data, congenital athymia was suspected and the patient received an allogenic cultured thymus tissue implant (CTTI). This is the first report of suspected congenital athymia and attempted treatment with CTTI associated with TP63 variant. At 9 months post-implant, peripheral lymphocyte analysis revealed measurable T cell receptor excision circles and presence of CD4+ recent thymic emigrants suggestive of early thymopoiesis. She will continue regular monitoring to ensure restoration of T cell immunity. [ABSTRACT FROM AUTHOR]

Aim: AMP‐activated protein kinase (AMPK) is activated during cellular energy perturbation. AMPK complexes are composed of three subunits and several variants of AMPK are expressed in skeletal muscle. The regulatory AMPKγ3 subunit is predominantly expressed in fast‐twitch muscle fibers. A human AMPKγ3 R225W mutation has been described. The mutation increases the total pool of AMPK activity in cells cultured from R225W carrier muscle and is associated with increased glycogen levels in mature skeletal muscle. This led to the idea of AMPKγ3 being involved in the regulation of skeletal muscle glycogen levels. Evidence for this causative link remains to be provided. Methods: We studied muscle biopsies from human carriers of the AMPKγ3 R225W mutation and we developed a novel AMPKγ3 R225W knock‐in mouse model (KI HOM). Through in vitro, in situ, and ex vivo techniques, we investigated AMPK activity, AMPK function, and glycogen levels in skeletal muscle of humans and mice. Results: In human carriers, the basal AMPKγ3‐associated activity was reduced when assayed in the absence of exogenous AMP. No difference was observed when assayed under AMP saturation, which was supported by findings in muscle of KI HOM mice. Furthermore, effects of AICAR/muscle contraction on AMPKγ3‐associated activity were absent in KI HOM muscle. Muscle glycogen levels were not affected by the mutation in human carriers or in KI HOM mice. Conclusions: The AMPKγ3 R225W mutation does not impact the AMPK‐associated activity in human skeletal muscle and the mutation is not linked to glycogen accumulation. The R225W mutation ablates the AMPKγ3‐associated activation by AICAR/muscle contractions, presumably due to loss of nucleotide binding in the CBS 1 domain of AMPKγ3. [ABSTRACT FROM AUTHOR]