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Biomedical subjects

A Khan

Publications and source records attributed to A Khan.

At least 19 recordsLinked to original sources
PubMed2026

Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.

Cryptosporidium spp. are parasites that cause severe illness in vulnerable human populations. Obtaining pure and sufficient Cryptosporidium DNA from clinical and environmental samples is a challenging task. Oocysts shed in available fecal samples can be limited in quantity, require purification (biased towards dominant strains), and yield limited DNA (&#x2009;<&#x2009;40 fg/oocyst). Here, we use updated genomic sequences from a broad diversity of Cryptosporidium species that have been found to infect humans (C. cuniculus, C. hominis, C. meleagridis, C. parvum, C. tyzzeri, and C. viatorum) to develop and validate a set of 100,000 RNA baits (CryptoCap_100k) with the aim of enriching Cryptosporidium DNA from varied samples. Compared to unenriched libraries, CryptoCap_100k increases the percentage of reads mapping to target genome sequences, increases the depth and breadth of genome coverage, and facilitates analyses of genetic variants in many samples, while decreasing overall costs.

Cryptosporidium↗
PubMed2025

GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp.

Cryptosporidium spp. are parasites that cause severe illness in vulnerable human populations. Obtaining pure and sufficient Cryptosporidium DNA from clinical and environmental samples is a challenging task. Oocysts shed in available fecal samples can be limited in quantity, require purification (biased towards dominant strains), and yield limited DNA (<40 fg/oocyst). Here, we use updated genomic sequences from a broad diversity of human-infecting Cryptosporidium species ( C. cuniculus , C. hominis , C. meleagridis , C. parvum , C. tyzzeri , and C. viatorum ) to develop and validate a set of 100,000 RNA baits (CryptoCap_100k) with the aim of enriching Cryptosporidium spp. DNA from varied samples. Compared to unenriched libraries, CryptoCap_100k increases the percentage of reads mapping to target genome sequences, increases the depth and breadth of genome coverage and the reliability of detecting species and mixed infections within a sample, and allows assessment of genetic variation via SNP calling, while decreasing costs.

Journal Article↗
PubMed2024

WHOLE GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING CRYPTOSPORIDIUM spp.

Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited DNA (<40 fg/oocyst). Here, we develop and validate a set of 100,000 RNA baits (CryptoCap_100k) based on six human-infecting Cryptosporidium spp. (C. cuniculus, C. hominis, C. meleagridis, C. parvum, C. tyzzeri, and C. viatorum) to enrich Cryptosporidium spp. DNA from a wide array of samples. We demonstrate that CryptoCap_100k increases the percentage of reads mapping to target Cryptosporidium references in a wide variety of scenarios, increasing the depth and breadth of genome coverage, facilitating increased accuracy of detecting and analyzing species within a given sample, while simultaneously decreasing costs, thereby opening new opportunities to understand the complex biology of these important pathogens.

Journal Article↗
PubMed2024

Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity.

Cryptosporidium is a leading cause of severe diarrhea and mortality in young children and infants in Africa and southern Asia. More than twenty Cryptosporidium species infect humans, of which C. parvum and C. hominis are the major agents causing moderate to severe diarrhea. Relatively few genetic markers are typically applied to genotype and/or diagnose Cryptosporidium. Most infections produce limited oocysts making it difficult to perform whole genome sequencing (WGS) directly from stool samples. Hence, there is an immediate need to apply WGS strategies to 1) develop high-resolution genetic markers to genotype these parasites more precisely, 2) to investigate endemic regions and detect the prevalence of different genotypes, and the role of mixed infections in generating genetic diversity, and 3) to investigate zoonotic transmission and evolution. To understand Cryptosporidium global population genetic structure, we applied Capture Enrichment Sequencing (CES-Seq) using 74,973 RNA-based 120 nucleotide baits that cover ~92% of the genome of C. parvum. CES-Seq is sensitive and successfully sequenced Cryptosporidium genomic DNA diluted up to 0.005% in human stool DNA. It also resolved mixed strain infections and captured new species of Cryptosporidium directly from clinical/field samples to promote genome-wide phylogenomic analyses and prospective GWAS studies.

Cryptosporidium↗
PubMed1992

Phyllodes tumours: a clinicopathological review of 30 cases.

Thirty cases of phyllodes tumour (cystosarcoma phyllodes) of the breast that presented to the Clinical Oncology Unit at Guy's Hospital were reviewed. Tumours were classified as benign, malignant or borderline according to the following histological criteria: mitotic rate, nuclear pleomorphism, stromal overgrowth and tumour margins. In 14 (46.5%) cases the tumours were considered histologically benign, in 11 (36.5%) malignant, and in five (17%) borderline. Recurrence was seen in a similar proportion of patients with tumours classified as benign (21%) and malignant (18%) according to histological criteria. Malignant lesions tended to recur earlier. Infiltrating tumour margins were noted in all patients and stromal overgrowth in all but one in whom recurrence was observed. Risk of recurrence also appeared to be related to tumour size. Only one patient developed distant metastases and died of her disease. Because of treatment variation no conclusion can be made regarding optimal therapy but the importance of adequate clearance, either through wide excision or mastectomy, is emphasized for all phyllodes tumours irrespective of histological features.

Adult↗
PubMed1979

Renal pedicle injury in the multiple injured patient.

Renal pedicle injuries were associated with multiple system trauma and a mortality rate of 42 per cent in 31 patients seen from 1959 to 1978. These injuries were to the renal artery in 14 patients, branches of the renal artery in 5, renal vein in 8, and renal artery and vein in 4. Priority of treatment for life-threatening associated injuries resulted in delayed diagnosis of the renal pedicle injury, which was not optimal for preservation of functioning renal tissues. Since 1968 an immediate excretory urogram has been performed for hematuria or a perirenal hematoma found during laparotomy for associated injuries. This study has resulted in the early diagnosis of renal pedicle injuries and immediate vascular repair has been attempted in 6 patients. Three of these patients survived with no hypertension on followup. A repaired renal vein in 1 patinet resulted in normal renal function and renal arteries were repaired in the other 2 patients with reduced renal function.

Adolescent↗
PubMed1979

Immunosuppressive effects of sulfato-trans-(-)-1,2-diaminocyclohexaneplatinum(II).

Sulfato-trans-(-)-1,2-diaminocyclohexane platinum(II) is a new antitumor agent. Its effect on immune responses was investigated. This agent inhibited lymphocyte transformation in response to phytohemagglutinin, pokeweed mitogen, and concanavalin A. It inhibited antibody plaque-forming spleen cells in AKR/J mice at doses ranging from 2.5 to 7.5 mg/kg i.p. It also prolonged the survival of skin grafts against major histocompatibility barriers in C57BL/6J mice transplanted with tail skin from CBA/J mice. The effective dose ranged from 2.5 to 5 mg/kg. This compound inhibited graft-versus-host reaction in three-week-old AKR/J X DBA/2JF1 mice receiving spleen cells from AKR/J mice i.p. Significant inhibition of graft-versus-host reaction was seen with doses ranging from 1 to 7.5 mg/kg i.p. These results suggest that this drug is immunosuppressive.

Animals↗