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PubMed2024

Identification of four TTN variants in three families with fetal akinesia deformation sequence.

BACKGROUND: TTN is a complex gene with large genomic size and highly repetitive structure. Pathogenic variants in TTN have been reported to cause a range of skeletal muscle and cardiac disorders. Homozygous or compound heterozygous mutations tend to cause a wide spectrum of phenotypes with congenital or childhood onset. The onset and severity of the features were considered to be correlated with the types and location of the TTN variants. METHODS: Whole-exome sequencing was performed on three unrelated families presenting with fetal akinesia deformation sequence (FADS), mainly characterized by reduced fetal movements and limb contractures. Sanger sequencing was performed to confirm the variants. RT-PCR analysis was performed. RESULTS: TTN c.38,876-2 A > C, a meta transcript-only variant, with a second pathogenic or likely pathogenic variant in trans, was observed in five affected fetuses from the three families. Sanger sequencing showed that all the fetal variants were inherited from the parents. RT-PCR analysis showed two kinds of abnormal splicing, including intron 199 extension and skipping of 8 bases. CONCLUSIONS: Here we report on three unrelated families presenting with FADS caused by four TTN variants. In addition, our study demonstrates that pathogenic meta transcript-only TTN variant can lead to defects which is recognizable prenatally in a recessive manner.

Humans↗

PubMed2003

Enteric campylobacter: purging its secrets?

Campylobacterial infections are the most common cause of bacterial enterocolitis in humans. Among children, especially in developing countries, Campylobacter infections can cause severe life-threatening diarrheal disease. Although usually associated with a benign outcome in the developed world, the burden of illness posed by Campylobacter infections is enormous, and serious neurologic sequelae also can occur. For a variety of reasons our understanding of the molecular and cellular pathogenesis of Campylobacter infection has lagged far behind that of other enteric pathogens. However, recent completion of the genome sequence of Campylobacter jejuni promises to open up the Campylobacter research field with the prospect of developing novel therapeutic and preventive strategies.

Campylobacter Infections↗

PubMed2003

Classical mitochondrial phenotypes without mtDNA mutations: the possible role of nuclear genes.

The authors analyzed the total mitochondrial (mt) genome in 15 patients with classic mitochondrial phenotypes. Novel somatic mtDNA mutations in two patients with chronic progressive external ophthalmoplegia were identified. Total automated mtDNA genome analysis did not reveal other pathogenic mtDNA mutations. The authors conclude that classic mitochondrial phenotypes, including those with adult onset, may occur in the absence of mtDNA mutations. Nuclear gene mutations may be the cause.

Cell Nucleus↗

PubMed2003

Protein prenyltransferases: anchor size, pseudogenes and parasites.

Lipid modification of eukaryotic proteins by protein prenyltransferases is required for critical signaling pathways, cell cycle progression, cytoskeleton remodeling, induction of apoptosis and vesicular trafficking. This review analyzes the influence of distinct states of sequential posttranslational processing that can be obtained after single or double prenylation, reversible palmitoylation, proteolytic cleavage of the C-terminus and possible reversible carboxymethylation. This series of modifications, as well as the exact length of the prenyl anchor, are determinants in protein-membrane and specific protein-protein interactions of protein prenyltransferase substrates. Furthermore, the occurrence and distribution of pseudogenes of protein prenyltransferase subunits are discussed. Besides being developed as anti-cancer agents, prenyltransferase inhibitors are effective against an increasing number of parasitic diseases. Extensive screens for protein prenyltransferases in genomic data of fungal and protozoan pathogens unveil a series of new pharmacologic targets for prenyltransferase inhibition, including the parasites Brugia malayi, Onchocerca volvulus, Aspergillus nidulans, Pneumocystis carinii, Entamoeba histolytica, Strongyloides stercoralis, Trichinella spiralis and Cryptosporidium parvum.

Animals↗

PubMed2004

Derivation, growth and applications of human embryonic stem cells.

Human embryonic stem (hES) cells are pluripotent cells derived from the inner cell mass cells of blastocysts with the potential to maintain an undifferentiated state indefinitely. Fully characterised hES cell lines express typical stem cell markers, possess high levels of telomerase activity, show normal karyotype and have the potential to differentiate into numerous cell types under in vitro and in vivo conditions. Therefore, hES cells are potentially valuable for the development of cell transplantation therapies for the treatment of various human diseases. However, there are a number of factors which may limit the medical application of hES cells: (a) continuous culture of hES cells in an undifferentiated state requires the presence of feeder layers and animal-based ingredients which incurs a risk of cross-transfer of pathogens; (b) hES cells demonstrate high genomic instability and non-predictable differentiation after long-term growth; and (c) differentiated hES cells express molecules which could cause immune rejection. In this review we summarise recent progress in the derivation and growth of undifferentiated hES cells and their differentiated progeny, and the problems associated with these techniques. We also examine the potential use of the therapeutic cloning technique to derive isogenic hES cells.

Blastocyst↗

PubMed2026

Acute respiratory viral diseases in Amazonas, Brazil: epidemiological patterns and implications for health surveillance.

BACKGROUND: Acute respiratory viral diseases are a major public health challenge in the Brazilian Amazon, where ecological, logistical, and social factors shape patterns of transmission and response. METHODS: This study aimed to analyze the epidemiological patterns and temporal-spatial distribution of Influenza-like illness (ILI) and severe acute respiratory syndrome (SARS) in the state of Amazonas, Brazil, between 2015 and 2025, distinguishing SARS-CoV-2 and non-SARS-CoV-2 etiologies using data from OpenDataSUS. RESULTS: Incidence peaks occurred in early 2021 and 2022, with pronounced regional disparities. The highest burdens were concentrated in specific municipalities, with Manaus exhibiting an intermediate incidence and playing a central role in case notifications and healthcare provision. DISCUSSION: We describe the integration of surveillance systems, laboratory networks, and healthcare infrastructure, which enabled improvements in diagnosis, monitoring, and care. The region's response model, centered in Manaus, includes primary-to-tertiary care coordination, molecular diagnostics, telemedicine, and mobile health units for Indigenous and remote areas. Research efforts during the COVID-19 pandemic provided critical insights into therapeutic strategies, immunopathology, and long-term sequelae, while also highlighting persistent inequities and diagnostic gaps. Our findings underscore the co-circulation of multiple respiratory pathogens and the need for continued genomic and syndromic surveillance. Future strategies must address regional disparities, support decentralized diagnostics, and expand clinical research. Strengthening integrated health systems in the Brazilian Amazon is essential for timely, equitable responses to emerging respiratory threats.

Brazil↗

PubMed2006

How influenza's neuraminidase promotes virulence and creates localized lung mucosa immunodeficiency.

Neuraminidase (NA) is an enzyme coded for by the genome of influenza critical for its pathogenicity and survival. Three currently accepted roles for this NA in promoting influenza virulence are: 1. NA cleaves newly formed virus particles from the host cell membrane. Without NA, newly formed virus would remain attached to the cell within which it was produced. 2. NA prevents newly released virus particles from aggregating to each other, preventing clumping that would reduce dissemination. 3. NA promotes viral penetration of sialic acid-rich mucin that bathes and protects respiratory epithelium through which the virus must spread and replicate. We outline here previous research evidence of two further, albeit hypothetical, functions of NA that together could cause disruption the mucosa-IgA axis, creating localized partial immunosuppressed state, enhancing both influenza infection itself and secondary bacterial pneumonia: 4. IgA provides primary immunoglobulin defense of mucosal surfaces. The hinge region of IgA is normally sialylated. IgA denuded of sialic acid is recognized, bound, and cleared by hepatic asialoglycoprotein receptor (ASGPR). Thus, IgA exposed to free NA would be so denuded and have increased hepatic clearance. 5. NA removes sialic acid moieties from mucosa-residing gamma/delta T cells or IgA producing B cells. Previous work indicates desialylation of these lymphocytes' outer cell membrane results in altered homing, to bone marrow, away from mucosa. Currently marketed NA inhibitors oseltamivir (Tamiflu) and zanamivir (Relenza) are FDA approved in USA for influenza prophylaxis and treatment. These NA inhibitors lower incidence of secondary bacterial infection in cases where an influenza infection occurs despite their use. Moreover, they are ameliorative in patients with secondary bacterial infections treated with antibiotics, a benefit that surpasses the treatment of antibiotics alone. We interpret these last two points as indicating our ascription of localized immunosuppression to influenza's NA could be correct and lead to new treatments of infections generally.

Animals↗

PubMed2026

X-linked hyper-IgM syndrome presenting as severe Pneumocystis pneumonia in a 6-month-old infant: a case report.

BACKGROUND: X-linked hyper-immunoglobulin M (XHIGM) syndrome is a rare primary immunodeficiency caused by mutations in the CD40 ligand gene (CD40LG), characterized by defective T-cell-dependent B-cell class-switch recombination. Patients typically present with recurrent infections in early childhood, but diagnosis is often delayed due to heterogeneous clinical manifestations and the fact that serum IgM levels may remain within the normal range in a significant proportion of patients. Here we report a case of XHIGM in an infant whose diagnostic journey began with recurrent lymphadenitis and culminated in life-threatening Pneumocystis jirovecii pneumonia (PJP). CASE PRESENTATION: A 6-month-old male infant was admitted with severe respiratory distress and hypoxemia. He had recurrent axillary lymphadenitis at 1 and 2 months of age and significant failure to thrive. Chest CT showed bilateral consolidative and interstitial opacities. Immunological evaluation revealed markedly decreased IgA, normal IgM and IgG, and profound T-cell lymphopenia. Sputum metagenomic sequencing identified Pneumocystis jirovecii. Whole-genome sequencing identified a hemizygous likely pathogenic CD40LG mutation (NM_000074.3:c.520C>T, p.Q174*); his mother was a carrier. He was treated with mechanical ventilation, trimethoprim-sulfamethoxazole (TMP-SMX), micafungin, corticosteroids, and intravenous immunoglobulin (IVIG), and was discharged after 36 days. CONCLUSIONS: In infants with recurrent or opportunistic infections, persistently low IgA and declining T-cell counts-even when initial screening appears normal-should raise suspicion for underlying immunodeficiency and prompt genetic evaluation. Early aggressive management and evaluation for hematopoietic stem cell transplantation are essential to improve outcomes.Serial immunological evaluation is essential in infants with recurrent or opportunistic infections, as persistently low IgA and declining T-cell counts-even when initial screening appears normal-should prompt genetic evaluation for underlying immunodeficiency. Early aggressive management and evaluation for hematopoietic stem cell transplantation are essential to improve outcomes.

Humans↗

PubMed2026

Deciphering the Role of LNX2 as a Potential Contributor to Neurodevelopmental Disorders.

BACKGROUND/OBJECTIVES: Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental condition characterized by a complex and multifactorial genetic architecture. In this study, we report a male patient, born to non-consanguineous healthy parents, presenting with ADHD and oppositional defiant disorder (ODD). METHODS: Trio-based whole-exome sequencing (WES) was performed in the proband and both parents. Variant classification was performed according to American College of Medical Genetics and Genomics (ACMG) guidelines, and the potential pathogenicity of the identified variant was further assessed through multiple in silico prediction algorithms and protein structural analyses. RESULTS: WES identified a homozygous variant in the LNX2 gene (NM_153371.4: c.1165G>A, p.Ala389Thr), classified as a variant of uncertain significance (VUS) and supported by multiple in silico predictions. LNX2 is expressed during brain development and encodes an E3 ubiquitin ligase involved in neuronal differentiation and synaptic function. The identified variant is located within the PDZ2 domain, a functionally relevant region involved in protein-protein interactions. Although the variant is reported in population databases (gnomAD ID: rs148429804), it has not been associated with any clinical phenotype, and its presence in the homozygous state has been reported only once, remaining extremely rare and lacking clinical annotation. Structural modelling predicted localized rearrangement of the hydrogen-bonding network within the PDZ2 domain without major conformational changes. Integrative transcriptomic, and single-cell analyses further supported the biological relevance of LNX2 in neurodevelopment, highlighting its preferential association with neuronal projection-cell networks, synaptic vesicle trafficking pathways, and neuron-specific regulatory programs. CONCLUSION: Although the identified LNX2 variant cannot be considered causative for the patient's phenotype and a definitive disease-gene relationship cannot be established based on a single individual, the complementary genetic, structural, and transcriptomic findings support the biological plausibility of LNX2 as a candidate gene for neurodevelopmental disorders. Additional independent patients and functional studies will be required to clarify its contribution to human disease.

Child↗

PubMed2026

CRISPR/Cas9-Mediated Site-Directed Mutagenesis of Genes in Klebsiella pneumoniae.

Constructing target-gene mutants with a common genetic background is crucial for elucidating gene function in antimicrobial resistance (AMR) research. Taking advantage of the single-guide RNA (sgRNA) and protospacer adjacent motif (PAM) sequence (3'-NGG) specificity of the Cas9 protein in the CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system and codon degeneracy, the authors design a repair template that incorporates the desired point mutation while excluding the PAM sequence disrupted by a synonymous substitution, thereby preventing re-cleavage by CRISPR/Cas9. This method employs two available plasmids, pCasKP-apr and pSGKP-spe, offering straightforward operation and high screening specificity. As a result, the approach enables efficient generation of genetically defined mutant strains of Klebsiella pneumoniae (K. pneumoniae) and is readily adaptable to routine laboratory settings. Furthermore, the protocol minimizes off-target editing, shortens experimental timelines, reduces screening workload, and provides a reliable platform for investigating resistance mechanisms, validating candidate genes, and supporting functional genomics studies in clinically relevant bacterial pathogens.

Klebsiella pneumoniae↗

PubMed2004

SCE jumping: genetic tool for allelic exchange in bacteria.

As more microbial genome sequence information becomes available, the field of bacterial pathogenesis would benefit from the development of new genetic tools designed to facilitate gene function studies on a genomic scale. The complete DNA sequence of the bacterium Pseudomonas aeruginosa provides an opportunity to apply functional genomics to a major opportunistic human pathogen. Here, I describe the development of a new gene replacement scheme termed "SCE jumping" in P. aeruginosa. The system uses the yeast I-SceI homing endonuclease in conjunction with in vitro mariner-transposon mutagenesis to generate mutations within targeted regions of the chromosome for genetic footprinting. Use of SCE jumping for generating transposon insertion mutants is anticipated to be widely applicable to other bacterial organisms. This allelic exchange strategy is discussed in context with other methods of gene replacement strategies available in P. aeruginosa. Development of SCE jumping provides an excellent example of the power of importing systems from unrelated organisms to circumvent practical challenges in molecular genetics.

Alleles↗

PubMed1986

The multifaceted retrovirus.

I have attempted to illustrate the many different properties of retroviruses and their presence in a wide variety of animal species including humans. Since the turn of this century, progress in the field of retrovirology has been noteworthy and many new and important scientific observations have been made (Table 7). Along the way, certain dogmas were replaced with new tenets. The recent recognition of retroviruses associated with human cancer and immunodeficiency places them into consideration as potential agents responsible for other human diseases such as autoimmunity and multiple sclerosis. Not only can retroviruses be oncogenic or cytopathic agents but they can also exist highly conserved as endogenous genes in the chromosomal DNA of many different species and not cause disease. In fact, this latter group appears to be predominant, suggesting their role in normal developmental processes and as progenitors of the pathogenic types. The virus-like genomes recognized in Drosophila and other lower animal species could be examples of this fact and may represent important biological entities throughout nature. The genetic material of retroviruses resembles transposons and may reflect the ability of these viruses to be passed within the host and to affect the evolutionary pathway. They could, as transposable elements, be transmitted as well to many different animal species. By their ability to move within the genetic machinery of the cell, these viruses could influence development in animals through promotion, enhancement, or suppression of specific cellular genes. This idea has been proposed for the noninfectious type A particles that have been observed to show these effects in cultured cells. One important observation is that the effect of retroviruses on cells has a varied pattern which may be emphasized by one group (e.g., vacuolization by foamy virus) or shared by other groups (e.g.., syncytial cell formation by type C and type D oncovirinae, spumavirinae, and lentivirinae) (Table 6). Moreover, the heterogeneity of the lentiviruses and the transduction of normal cellular genes by many of the oncogenic viruses indicate the changes that can occur as retroviruses infect and replicate within the cell. The overview is very informative. Virus-cell interaction can lead to biological expressions that depend on the phenotype of the cell and the viral genetic structure. Throughout its existence in nature the retrovirus has been evolving, conserving certain features while developing new ones with different properties; it clearly emerges as a multifaceted agent.

Animals↗

PubMed2025

Genomic testing for RET in the clinic: UK and global perspective.

RET is a key oncogene in neuroendocrine cancer. Pathogenic germline variants lead to multiple different phenotypes, including multiple endocrine neoplasia type 2, medullary thyroid cancer (MTC), Hirschsprung disease and kidney malformations. Pathogenic somatic variants are also associated with MTC, and RET rearrangements are observed in papillary thyroid cancer, non-small cell lung cancer and pan-cancer syndromes. Testing for both germline and somatic variants is now feasible in everyday clinical practice, and their identification has important clinical consequences, both for affected individuals and their families. This mini-review will discuss current germline and somatic testing strategies in the UK and worldwide, as well as reporting and test outcomes (including variants of uncertain significance or incidental findings). It will explore actions following identification of a pathogenic germline variant, including predictive, reproductive and childhood testing, and somatic testing of RET variants in solid tumours informing personalised cancer treatment. Finally, it will discuss the challenge of delivering rapid and equitable access to genomic testing to ensure that all individuals can benefit promptly and appropriately to improve clinical outcomes.

Humans↗

PubMed2003

[Genomic characterization of SARS coronavirus: a novel member of coronavirus].

In March 2003, SARS-CoV, a novel coronavirus which has been proved to be a pathogen causing Severe Acute Respiratory Syndrome (SARS). The complete genome of SARS-CoV has been sequenced by international collaboration including China. In the present study, the genome sequences were collected from NCBI and genomic characterization was analyzed. SARS-CoV has a genome of 28-30 kb including 11 ORFs (Open Reading Frames), which is consistent with that of coronavirus family, and its genome organization is similar to those of other coronaviruses as well. SARS-CoV evolutionally closes to other coronavirus in their corresponding proteins, such as spike protein, small membrane protein and nucleocapsid protein. In some regions of the genome, the genomic sequence of SARS-CoV was significantly different from that of other coronavirus, and has a self-conservative genomic sequence. Moreover, its encoding protein sequences were greatly different from those of other coronavirus. The analysis indicated that SARS-CoV has lower redundancy, that is, it has a high variation possibility. It may not be a variant of other coronaviruses but a novel coronavirus, which existed independently in nature and was not recognized by human being before, although SARS-CoV is morphologically similar to other coronavirus and belongs to coronavirus family. The sequences of its genes and encoding proteins are substantially different from those of other coronavirus.

Coronavirus↗

PubMed2003

[Role of horizontal gene transfer by bacteriophages in the origin of pathogenic bacteria].

The review considers the involvement of bacteriophages in transferring genes, which determine bacterial pathogenicity, and the increasing role of comparative genomics and genetics of bacteria and bacteriophages in detecting new cases of horizontal gene transfer. Examples of phage participation in this process proved to a different extent are described. Emphasis is placed on the original work carried out in Russia and focused on bacteriophages (temperate transposable phages and giant virulent phi KZ-like phages) of conditional pathogen Pseudomonas aeruginosa. Consideration is given to the possible lines of further research of the role of bacteriophages in the infection process and, in particular, the role of virulent phages, whose products are similar to those of pathogenic bacteria, in modification of clinical signs of infectious diseases and in evolution. An attempt is made to predict the possible direction of pathogen evolution associated with development of new treatment strategies and generation of new specific niches.

Animals↗

PubMed2005

Respiratory pathogens in dental plaque of hospitalized patients with chronic lung diseases.

Bacterial cultivation studies have shown that dental plaque is a reservoir for respiratory pathogens in intensive care unit patients and in elderly who are debilitated, hospitalized or in a nursing home, placing them at risk of bacterial pneumonia. No information is available, however, concerning dental plaque as a reservoir of putative respiratory pathogens in hospitalized patients with chronic lung diseases. Supragingival plaque colonization of 34 hospitalized chronic lung-diseased Romanian citizens, excluding those with tuberculosis and less than 20 teeth, was therefore assessed by checkerboard DNA-DNA hybridization using a selected panel of whole genomic DNA probes produced from eight respiratory pathogens and eight oral pathogens. Thirty-one lung-healthy dental outpatients served as reference population. Respiratory pathogens were detected in plaque from 29 of the 34 (85.3%) hospitalized patients and 12 of the 31 (38.7%) reference population subjects. Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacter cloacae occurred significantly (p<0.05) more frequent among the hospitalized patients. Hospitalized chronic lung-diseased patients harbored in their supragingival plaque samples bacteria known to cause nosocomial pneumonia significantly (p<0.001) more frequent than lung-healthy dental outpatients. Our results indicate that dental plaque in patients with chronic lung diseases often serves as a reservoir of bacteria known to cause nosocomial pneumonia in susceptible individuals.

Adult↗

PubMed2004

Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex.

To better understand the biology and the virulence determinants of the two major mycobacterial human pathogens Mycobacterium tuberculosis and Mycobacterium leprae, their genome sequences have been determined recently. In silico comparisons revealed that among the 1439 genes common to both M. tuberculosis and M. leprae, 219 genes code for proteins that show no similarity with proteins from other organisms. Therefore, the latter 'core' genes could be specific for mycobacteria or even for the intracellular mycobacterial pathogens. To obtain more information as to whether these genes really were mycobacteria-specific, they were included in a focused macro-array, which also contained genes from previously defined regions of difference (RD) known to be absent from Mycobacterium bovis BCG relative to M. tuberculosis. Hybridization of DNA from 40 strains of the M. tuberculosis complex and in silico comparison of these genes with the near-complete genome sequences from Mycobacterium avium, Mycobacterium marinum and Mycobacterium smegmatis were undertaken to answer this question. The results showed that among the 219 conserved genes, very few were not present in all the strains tested. Some of these missing genes code for proteins of the ESAT-6 family, a group of highly immunogenic small proteins whose presence and number is variable among the genomically highly conserved members of the M. tuberculosis complex. Indeed, the results suggest that, with few exceptions, the 'core' genes conserved among M. tuberculosis H37Rv and M. leprae are also highly conserved among other mycobacterial strains, which makes them interesting potential targets for developing new specific anti-mycobacterial drugs. In contrast, the genes from RD regions showed great variability among certain members of the M. tuberculosis complex, and some new specific deletions in Mycobacterium canettii, Mycobacterium microti and seal isolates were identified and further characterized during this study. Together with the distribution of a particular 6 or 7 bp micro-deletion in the gene encoding the polyketide synthase pks15/1, these results confirm and further extend the revised phylogenetic model for the M. tuberculosis complex recently presented.

Antigens, Bacterial↗

PubMed2005

Application of a spotting sample preparation technique for the detection of pathogens in woody plants by RT-PCR and real-time PCR (TaqMan).

An extraction technique for reverse transcription-PCR (RT-PCR) detection of plant pathogens including viruses, bacteria and phytoplasma is described. The total nucleic acid of these plant pathogens was obtained by direct spotting of crude sap derived from infected leaf, petiole or cambial tissue onto two different types of membranes, positively charged Hybond N(+) Nylon and FTA membranes, and processed for use in PCR. Thirteen different plant viruses, Xylella fastidiosa (causal agent of Pierce's disease) and phytoplasmas were included in the experiment. A thermal treatment (95 degrees C for 10 min) of the Hybond N(+) Nylon discs in a buffered solution improved the detection, but for FTA membrane discs the thermal treatment was not required and the discs were directly placed in the PCR reaction cocktail. Specific amplification of genomic or ribosomal RNA fragments of these pathogens was obtained by one-step RT-PCR except for X. fastidiosa in which a fragment of the genomic DNA was used for amplification. The same sample preparation methods also worked well for real-time RT-PCR (TaqMan). The sample preparation techniques reported here could be used to store samples for future PCR test or for long distance shipment to a detection laboratory.

Edetic Acid↗