Investigating the effects of a single ASPM variant (c.8508_8509) on brain architecture among siblings in a consanguineous Pakistani family

BACKGROUND

Autosomal Recessive Primary Microcephaly (MCPH) is a rare, neurodevelopmental disorder associated with mild to severe mental retardation. It is characterized by reduced cerebral cortex that ultimately leads to reduction in skull size less than - 3 S.D below the mean for normal individuals having same age and sex. Till date, 30 known loci have been reported for MCPH.

METHODS

In the present study, Sanger sequencing was performed followed by linkage analysis to validate the mutation in ASPM gene of the consanguineous Pakistani clans. Bioinformatics tools were also used to confirm the pathogenicity of the diseased variant in the gene. MRI scan was used to compare the brain structure of both the affected individuals (Aslam et al. in Kinnaird's 2nd International Conference on Science, Technology and Innovation, Lahore, 2023).

RESULTS

Our study described a consanguineous family with two patients with a known ASPM (MCPH5) variant c.8508_8509delGA causing a frameshift mutation in exon 18 which located in calmodulin-binding IQ domain of the ASPM protein. The salient feature of this study is that a single variant led to significantly distinct changes in the architecture of brain of both siblings which is further confirmed by MRI results. The computation analysis showed that the change in the conservation of this residue cause this variant highly pathogenic. Carrier screening and genetic counselling were also remarkable features of this study (Aslam et al. in Kinnaird's 2nd International Conference on Science, Technology and Innovation, Lahore, 2023).

CONCLUSION

This study explores the extraordinary influence of a single ASPM variant on divergent brain structure in consanguineous siblings and enable us to reduce the incidence of further microcephalic cases in this Pakistani family (Aslam et al. in Kinnaird's 2nd International Conference on Science, Technology and Innovation, Lahore, 2023).

Genetic susceptibility of vitamin D receptor gene polymorphisms on autosomal recessive primary microcephaly patients in Pakistani population: a case-control and in-silico study

BACKGROUND

Autosomal recessive primary microcephaly (MCPH) is a rare genetic disorder that leads to reduced cerebral cortex caused by a mutation in corticogenesis. The expression of the Vitamin D receptor (VDR) gene is involved in the proliferation and differentiation of neural stem cells, and VDR polymorphisms have been associated with various neurological disorders. However, their relationship with MCPH has not been explored. This study aimed to investigate the association of VDR polymorphisms with MCPH due to its role in Wnt signaling pathway and its In-silico analysis.

METHODS

Blood samples of 64 MCPH patients and 52 controls were collected to genotype VDR SNPs (TaqI (rs731236), FokI (rs2228570) and BsmI (rs1544410). In-silico tools were also used to assess the effects of exonic SNPs on mRNA and protein structure and pathogenicity of exonic and intronic SNPs.

RESULTS

The study found that serum 25-OH vitamin D3 levels were significantly different in MCPH patients and healthy controls (P = 0.000). The genetic analysis showed that VDR polymorphisms of FokI and BsmI were seven times more frequent in MCPH patients than in controls (P < 0.05) and the recessive model for TaqI and dominant model for BsmI polymorphisms were also associated with the pathogenesis of MCPH. In-silico analysis showed that the pathogenicity effects of rs2228570 and rs1544410 are neutral while rs731236 causes a silent mutation which has no effect on VDR protein.

CONCLUSION

VDR polymorphisms of FokI and BsmI are associated with the risk of MCPH. These findings suggest that VDR polymorphisms play a role in MCPH, which could provide important insights for understanding the molecular mechanisms of the disease.

Exome Sequencing Reveals SLC4A11 Variant Underlying Congenital Hereditary Endothelial Dystrophy (CHED2) Misdiagnosed as Congenital Glaucoma

Autosomal recessive congenital hereditary endothelial dystrophy (CHED2) may be misdiagnosed as primary congenital glaucoma (PCG) due to similar clinical phenotypes during early infancy. In this study, we identified a family with CHED2, which was previously misdiagnosed as having PCG, and followed up for 9 years. Linkage analysis was first completed in eight PCG-affected families, followed by whole-exome sequencing (WES) in family PKGM3. The following in silico tools were used to predict the pathogenic effects of identified variants: I-Mutant 2.0, SIFT, Polyphen-2, PROVEAN, mutation taster and PhD-SNP. After detecting an SLC4A11 variant in one family, detailed ophthalmic examinations were performed again to confirm the diagnosis. Six out of eight families had CYP1B1 gene variants responsible for PCG. However, in family PKGM3, no variants in the known PCG genes were identified. WES identified a homozygous missense variant c.2024A>C, p.(Glu675Ala) in SLC4A11. Based on the WES findings, the affected individuals underwent detailed ophthalmic examinations and were re-diagnosed with CHED2 leading to secondary glaucoma. Our results expand the genetic spectrum of CHED2. This is the first report from Pakistan of a Glu675Ala variant with CHED2 leading to secondary glaucoma. The p.Glu675Ala variant is likely a founder mutation in the Pakistani population. Our findings suggest that genome-wide neonatal screening is worthwhile to avoid the misdiagnosis of phenotypically similar diseases such as CHED2 and PCG.

MHD Pulsatile Flow of Blood-Based Silver and Gold Nanoparticles between Two Concentric Cylinders

Pulsatory movements appear in a variety of fascinating applications involving periodic flow propagation and control. Pulsing encourages mixing and, as a result, mass and heat exchange with the boundaries. Pulsing also helps to decrease surface fouling by allowing solid particles to migrate. An exact solution of the Navier–Stokes equations for the transport of an incompressible viscous fluid in a channel with arbitrary pressure distribution is described in this study. The flow is defined by two primary parameters: the pulsation parameter, which is determined by the periodic pressure gradient, and the kinetic Reynolds number, which is determined by the pulsation frequency. The purpose of employing hybrid nanofluid (HNF) is to increase the base fluid’s thermal conductivity. We regard Ag and Au as nanoparticles (NPs) and blood as a base fluid for this phenomenon. Broadening this reveals that the consideration of nanoparticles has impressively extended the warm movement at the parcels of both turbulent and laminar frameworks. Attention is paid to the slope of speed, temperature, and voltage. The geometric model is therefore described using a symmetry technique. We developed the governing equation for this problem’s analytical solutions. The velocity and temperature fields solution is given in the form of the Bessel and modified Bessel functions. Graph results show the mathematical benefits of the current limits: for instance, Hartmann number M, solid volume part of nanoparticles ϕ, Reynolds number Reβ, Prandtl number Pr, intermittent slob limit, etc. The strain angles introduced in the stress contrast, frictional force, velocity profile, and temperature profile were obtained, and the characteristics of the vortex were investigated. Resources at various boundaries of the perceptual flow are examined. As with the final essence, the smoothest results are analyzed and recorded. It has also been discovered that the velocity may be regulated by the external magnetic field, which affects the temperature profiles and hence the heat transfer, which can be enhanced or lowered by mastering the magnetic field.

Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging

Existing three-dimensional (3D) culture techniques are limited by trade-offs between throughput, capacity for high-resolution imaging in living state, and geometric control. Here, we introduce a modular microscale hanging drop culture where simple design elements allow high replicates for drug screening, direct on-chip real-time or high-resolution confocal microscopy, and geometric control in 3D. Thousands of spheroids can be formed on our microchip in a single step and without any selective pressure from specific matrices. Microchip cultures from human LN229 glioblastoma and patient-derived mouse xenograft cells retained genomic alterations of originating tumors based on mate pair sequencing. We measured response to drugs over time with real-time microscopy on-chip. Last, by engineering droplets to form predetermined geometric shapes, we were able to manipulate the geometry of cultured cell masses. These outcomes can enable broad applications in advancing personalized medicine for cancer and drug discovery, tissue engineering, and stem cell research.

Evaluation of the cytotoxic and antiviral effects of ethanol extract of three Opuntia species of Peste des Petits ruminant virus

Purpose: To assess in vitro the virocidal effects of different species of cactus plant on the lethal action of Peste des petits virus (PPRV).Method: Ethanol extracts of different cactus plants were obtained. A serial twofold dilution of the extracts was prepared. Cytotoxic and antiviral activities were examined through MTT assay at various concentrations. Vero cell lines were grown in 96 well plates up to an 80 % confluent monolayer. The plates were divided into two groups, one for antiviral and the other for cytotoxicity activity. The cells were exposed to various concentrations of the ethanol extracts to assess the cytotoxicity, whereas to assess the antiviral activity, PPRV was re-incubated with the extracts and then exposed to cells. MMT dye was added and the results were evaluated as cell survival (%).Results: At higher concentrations, i.e., 500 - 1000 μg/mL, ethanol extracts from all the Opuntia species displayed cytotoxic effects. The ethanol extract of OM exhibited the greatest antiviral potential of all the extracts, while the extract of Opuntia stricta (OS) was the least effective against PPRV in the cultured cells. There were significant differences (p < 0.05) in the concentration of Opuntia manocantha (OM), Opuntia delinii OD and Opuntia stricta (OS) with reference to antiviral activity. OM showed antiviral activity against PPRV from 3.25 to 125 μg/mL, OD antiviral activity from 31.25 to 62.5 ug/ml whereas OS showed antiviral activity at 2.5 μg/mLConclusion: The ethanol extract of Opuntia species reduces the infection of PPRV in Caprine. Keywords: Cactus, Opuntia spp., Peste des petits ruminants virus (PPRV), Vero cell line

Spectrum of genetic variants in moderate to severe sporadic hearing loss in Pakistan

Hearing loss affects 380 million people worldwide due to environmental or genetic causes. Determining the cause of deafness in individuals without previous family history of hearing loss is challenging and has been relatively unexplored in Pakistan. We investigated the spectrum of genetic variants in hearing loss in a cohort of singleton affected individuals born to consanguineous parents. Twenty-one individuals with moderate to severe hearing loss were recruited. We performed whole-exome sequencing on DNA samples from the participants, which identified seventeen variants in ten known deafness genes and one novel candidate gene. All identified variants were homozygous except for two. Eleven of the variants were novel, including one multi-exonic homozygous deletion in OTOA. A missense variant in ESRRB was implicated for recessively inherited moderate to severe hearing loss. Two individuals were heterozygous for variants in MYO7A and CHD7, respectively, consistent with de novo variants or dominant inheritance with incomplete penetrance as the reason for their hearing loss. Our results indicate that similar to familial cases of deafness, variants in a large number of genes are responsible for moderate to severe hearing loss in sporadic individuals born to consanguineous couples.

Emergence of functional neuromuscular junctions in an engineered, multicellular spinal cord-muscle bioactuator

Three-dimensional (3D) biomimetic systems hold great promise for the study of biological systems in vitro as well as for the development and testing of pharmaceuticals. Here, we test the hypothesis that an intact segment of lumbar rat spinal cord will form functional neuromuscular junctions (NMJs) with engineered, 3D muscle tissue, mimicking the partial development of the peripheral nervous system (PNS). Muscle tissues are grown on a 3D-printed polyethylene glycol (PEG) skeleton where deflection of the backbone due to muscle contraction causes the displacement of the pillar-like "feet." We show that spinal cord explants extend a robust and complex arbor of motor neurons and glia in vitro. We then engineered a "spinobot" by innervating the muscle tissue with an intact segment of lumbar spinal cord that houses the hindlimb locomotor central pattern generator (CPG). Within 7 days of the spinal cord being introduced to the muscle tissue, functional neuromuscular junctions (NMJs) are formed, resulting in the development of an early PNS in vitro. The newly innervated muscles exhibit spontaneous contractions as measured by the displacement of pillars on the PEG skeleton. Upon chemical excitation, the spinal cord-muscle system initiated muscular twitches with a consistent frequency pattern. These sequences of contraction/relaxation suggest the action of a spinal CPG. Chemical inhibition with a blocker of neuronal glutamate receptors effectively blocked contractions. Overall, these data demonstrate that a rat spinal cord is capable of forming functional neuromuscular junctions ex vivo with an engineered muscle tissue at an ontogenetically similar timescale.

Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay details and primer sequences become widely known, many laboratories could perform diagnostic tests using methods such as RT-PCR or isothermal RT-LAMP amplification. A key advantage of RT-LAMP based approaches compared to RT-PCR is that RT-LAMP is known to be robust in detecting targets from unprocessed samples. In addition, RT-LAMP assays are performed at a constant temperature enabling speed, simplicity, and point-of-use testing. Here, we provide the details of an RT-LAMP isothermal assay for the detection of SARS-CoV-2 virus with performance comparable to currently approved tests using RT-PCR. We characterize the assay by introducing swabs in virus spiked synthetic nasal fluids, moving the swab to viral transport medium (VTM), and using a volume of that VTM for performing the amplification without an RNA extraction kit. The assay has a Limit-of-Detection (LOD) of 50 RNA copies/μL in the VTM solution within 20 minutes, and LOD of 5000 RNA copies/μL in the nasal solution. Additionally, we show the utility of this assay for real-time point-of-use testing by demonstrating detection of SARS-CoV-2 virus in less than 40 minutes using an additively manufactured cartridge and a smartphone-based reader. Finally, we explore the speed and cost advantages by comparing the required resources and workflows with RT-PCR. This work could accelerate the development and availability of SARS-CoV-2 diagnostics by proving alternatives to conventional laboratory benchtop tests.

Evaluation of bioherbicidal potential of Carica papaya leaves

Due to increased number of herbicide resistant weeds, it is needed to explore the allelopathic potential of plants as an alternative. The research was conducted to investigate allelopathic effects of Carica papaya L. leaf powder and aqueous extract on seeds as well as pre-germinated seeds of Avena fatua L., Helianthus annuus L., Rumex dentatus L., Zea mays L. and Triticum aestivum L. on filter paper and soil in Weed Management Program Laboratory, Department of Plant and Environmental Protection at PARC Institute of Advanced Studies in Agriculture, National Agriculture Research Centre, Islamabad, Pakistan. Germination percentage (%), radicle length (cm) and plumule length (cm) were parameters observed for 'Plant leaf powder bioassay' and 'Aqueous extract method'. Most significant growth inhibition was observed in A. fatua seedlings in filter paper method. A. fatua radicle length was reduced by C. papaya aqueous extract (80%) and leaf powder (89%) bioassays. Plumule length was reduced under the influence of aqueous extract (57-73%) and powdered material (59-77%). The inhibitory effects on other test species were in sequence of H. annuus followed by Z. mays and R. dentatus. The aqueous extract showed non-significant effect on wheat seed germination, radicle and plumule growth. It is suggested that C. papaya aqueous extract can be used as source of weed management in wheat crop.

CDC14A phosphatase is essential for hearing and male fertility in mouse and human

The Cell Division-Cycle-14 gene encodes a dual-specificity phosphatase necessary in yeast for exit from mitosis. Numerous disparate roles of vertebrate Cell Division-Cycle-14 (CDC14A) have been proposed largely based on studies of cultured cancer cells in vitro. The in vivo functions of vertebrate CDC14A are largely unknown. We generated and analyzed mutations of zebrafish and mouse CDC14A, developed a computational structural model of human CDC14A protein and report four novel truncating and three missense alleles of CDC14A in human families segregating progressive, moderate-to-profound deafness. In five of these families segregating pathogenic variants of CDC14A, deaf males are infertile, while deaf females are fertile. Several recessive mutations of mouse Cdc14a, including a CRISPR/Cas9-edited phosphatase-dead p.C278S substitution, result in substantial perinatal lethality, but survivors recapitulate the human phenotype of deafness and male infertility. CDC14A protein localizes to inner ear hair cell kinocilia, basal bodies and sound-transducing stereocilia. Auditory hair cells of postnatal Cdc14a mutants develop normally, but subsequently degenerate causing deafness. Kinocilia of germ-line mutants of mouse and zebrafish have normal lengths, which does not recapitulate the published cdc14aa knockdown morphant phenotype of short kinocilia. In mutant male mice, degeneration of seminiferous tubules and spermiation defects result in low sperm count, and abnormal sperm motility and morphology. These findings for the first time define a new monogenic syndrome of deafness and male infertility revealing an absolute requirement in vivo of vertebrate CDC14A phosphatase activity for hearing and male fertility.

Clinical variability of CYP1B1 gene variants in Pakistani primary congenital glaucoma families

OBJECTIVE

To explore the spectrum of Cytochrome P450 1B1 gene variants and genotype-phenotype correlations in families affected with primary congenital glaucoma.

METHODS

The cross-sectional study was performed at the Department of Biotechnology, Lahore College for Women University, Lahore, and the School of Biological Sciences, University of the Punjab, Lahore, Pakistan, from February 2015 to October 2016. Six consanguineous families having individuals affected with primary congenital glaucoma were recruited from different hospitals of the city. Sanger sequencing of coding exon of Cytochrome P450 1B1 gene was performed in order to identify the variants segregating with the disorder.

RESULTS

All six families had multiple individuals affected with primary congenital glaucoma. Five out of six families (83%, 5/6) showed CYP1B1 mutations upon Sanger sequencing.All eighteen patients of five families with homozygous Cytochrome P450 1B1 gene variants had different degrees of severity of the phenotypes. Clinical evaluation of the affected members revealed congenital glaucoma with a severe phenotype of corneal oedema, photophobia and corneal scarring. The onset of the phenotype was reported to be congenital but the clinical diagnosis was delayed in four cases since medical help was not sought by the families till much later.

CONCLUSIONS

The different degrees of severe phenotypes even in individuals with the same Cytochrome P450 1B1 gene mutation suggested the involvement of modifiers in reducing or increasing the disease severity.

Multivariate computational analysis of biosensor's data for improved CD64 quantification for sepsis diagnosis

Sepsis, as a leading cause of death worldwide, relies on systemic inflammatory response syndrome (SIRS) criteria for its diagnosis. SIRS is highly non-specific as it relies on monitoring of patients' vitals for sepsis diagnosis, which are known to change with many confounding factors. Changes in leukocyte counts and CD64 expression levels are known specific biomarkers of pro-inflammatory host response at the onset of sepsis. Recently, we have developed a biosensor chip that can enumerate the leukocyte counts and quantify the neutrophil CD64 expression levels from a drop of blood. We were able to show improved sepsis diagnosis and prognosis in clinical studies by measuring these parameters during different times of the patients' stay in hospital. In this paper, we investigated the rate of cell capture with CD64 expression levels and used this in a multivariate computational model using artificial neural networks (ANNs) and showed improved accuracy of quantifying CD64 expression levels from the biosensor (n = 106 whole blood experiments). We found a high coefficient of determination and low error between biosensor- and flow cytometry-based neutrophil CD64 expression levels using multiple ANN training methods in comparison to those of univariate regression commonly employed. This approach can find many applications in biosensor data analytics by utilizing multiple features of the biosensor's data for output determination.

Hands-free smartphone-based diagnostics for simultaneous detection of Zika, Chikungunya, and Dengue at point-of-care

Infectious diseases remain the world's top contributors to death and disability, and, with recent outbreaks of Zika virus infections there has been an urgency for simple, sensitive and easily translatable point-of-care tests. Here we demonstrate a novel point-of-care platform to diagnose infectious diseases from whole blood samples. A microfluidic platform performs minimal sample processing in a user-friendly diagnostics card followed by real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on the same card with pre-dried primers specific to viral targets. Our point-of-care platform uses a commercial smartphone to acquire real-time images of the amplification reaction and displays a visual read-out of the assay. We apply this system to detect closely related Zika, Dengue (types 1 and 3) and Chikungunya virus infections from whole blood on the same pre-printed chip with high specificity and clinically relevant sensitivity. Limit of detection of 1.56e5 PFU/mL of Zika virus from whole blood was achieved through our platform. With the ability to quantitate the target nucleic acid, this platform can also perform point-of-care patient surveillance for pathogen load or select biomarkers in whole blood.

Genetic causes of moderate to severe hearing loss point to modifiers

The genetic underpinnings of recessively inherited moderate to severe sensorineural hearing loss are not well understood, despite its higher prevalence in comparison to profound deafness. We recruited 92 consanguineous families segregating stable or progressive, recessively inherited moderate or severe hearing loss. We utilized homozygosity mapping, Sanger sequencing, targeted capture of known deafness genes with massively parallel sequencing and whole exome sequencing to identify the molecular basis of hearing loss in these families. Variants of the known deafness genes were found in 69% of the participating families with the SLC26A4, GJB2, MYO15A, TMC1, TMPRSS3, OTOF, MYO7A and CLDN14 genes together accounting for hearing loss in 54% of the families. We identified 20 reported and 21 novel variants in 21 known deafness genes; 16 of the 20 reported variants, previously associated with stable, profound deafness were associated with moderate to severe or progressive hearing loss in our families. These data point to a prominent role for genetic background, environmental factors or both as modifiers of human hearing loss severity.

Microbiological Load of Ethylene Oxide Sterilized Medical Devices and its Elimination by Cobalt 60 Source

OBJECTIVE

To determine the residing microbial flora of ethylene oxide (EtO) sterilized medical devices and optimization of safe dose of gamma radiation (Cobalt 60 source) for the complete elimination of microbial load.

STUDY DESIGN

Experimental study.

PLACE AND DURATION OF STUDY

Department of Biotechnology, Lahore College for Women University, Lahore, Pakistan from September 2014 to June 2015.

METHODOLOGY

Thirty-six samples of EtO sterilized medical devices of same batch of three different companies were collected for this study. Isolation and enumeration of microbes were done by using different selective and differential media. Gram staining and biochemically characterization by API 20 (Bio Merieux, France) kit was done for identification of the microorganisms. The medical devices having high microbial load were sent to Pakistan Radiation Services (PARAS) for gamma irradiations at 3 different selected doses (20 KGy, 25 KGy, and 30 KGy).

RESULTS

Different types of Gram positive bacteria (Staphylococcus epidermidis, Staphylococcus aureus andBacillus subtilis) were isolated from the EtO sterilized samples. Gram negative bacteria and fungi were not detected on these medical devices. Gamma irradiations results showed that 30 KGy was optimized dose for complete elimination of microbial flora on endotracheal, Nelaton, and tracheostomy tubes.

CONCLUSION

Gamma radiations (Co 60 source) effectively decontaminate the microbial flora on the equipment previously sterilized by the ethylene oxide gas; and 30 KGy is the optimized dose for all these medical devices.

Serum Calcium Derangements in Neonates with Hypoxic Ischemic Encephalopathy (HIE) With and Without Therapeutic Hypothermia

BACKGROUND: Perinatal hypoxia is a recognized cause of hypocalcemia in neonates in the first 3 days of age. However, therapeutic hypothermia (TH), the standard care for moderate to severe HIE, promotes neuropro-tection by decreasing calcium (Ca) influx into the cells during reperfusion phase. So TH can increase serum Ca levels and may even negate the hypo-calcemic effects in HIE.

OBJECTIVES: To examine the trends in serum Ca levels in neonates with HIE with and without TH.

DESIGN/METHODS: A retrospective cohort study of neonates with moderate to severe HIE admitted to a level III NICU between September 2011 and October 2015. HIE staging was done as per modified Sarnat’s scoring system. Hypercalcemia was defined as serum ionised Ca (iCa) &gt;1.35 mmol/L and hypocalcemia was defined as serum iCa &lt;0.9 mmol/L. Acidosis was considered if pH &lt;7.2. Serum Ca and pH were followed in the first 3 days of age (Day 1-3). The relation of serum Ca levels with acidosis,seizures, intracranial hemorrhage, and MRI changes in neonates with and without TH was examined. Categorical variables were analysed using chi-square test. Logistic regression analysis was done to explore the association of hypo/hypercalcemia with various variables, adjusting for TH, HIE staging, and acidosis.

RESULTS: Total number of neonates with moderate-severe HIE= 113; 89 neonates (79%) underwent TH. Incidence of hypercalcemia was 57/89 (88%) in the TH group whereas only one-third in the no TH group, whereas for hypocalcemia, it was 11/89(12%) and 5/24(21%) for the TH and no TH groups respectively. Hypercalcemia on Day 1 was significantly higher with TH(p 0.007) and acidosis(p 0.015). Hypocalcemia did not have any such association. Hypo/hypercarbia did not seem to alter the serum Ca levels. There was no increase in intracranial hemorrhage, clinical/EEG seizures, antiepileptic drug use or hypoxic MRI changes with Ca derangements.

CONCLUSION: Incidence of hypocalcemia was reduced by almost half in TH group. Hypercalcemia on day 1 was significantly associated with TH and acidosis. On days 2 and 3, hypercalcemia occurred in TH even in the absence of acidosis, but the association was not statistically significant. Less hypocalcemia and more hypercalcemia in TH may be attributed to the neuroprotective effect of TH by inhibiting Ca influx into the cells. However, there was no correlation between Ca derangements and seizures or severity of hypoxic changes in MRI.

A microfluidic biochip for complete blood cell counts at the point-of-care

Complete blood cell counts (CBCs) are one of the most commonly ordered and informative blood tests in hospitals. The results from a CBC, which typically include white blood cell (WBC) counts with differentials, red blood cell (RBC) counts, platelet counts and hemoglobin measurements, can have implications for the diagnosis and screening of hundreds of diseases and treatments. Bulky and expensive hematology analyzers are currently used as a gold standard for acquiring CBCs. For nearly all CBCs performed today, the patient must travel to either a hospital with a large laboratory or to a centralized lab testing facility. There is a tremendous need for an automated, portable point-of-care blood cell counter that could yield results in a matter of minutes from a drop of blood without any trained professionals to operate the instrument. We have developed microfluidic biochips capable of a partial CBC using only a drop of whole blood. Total leukocyte and their 3-part differential count are obtained from 10 μL of blood after on-chip lysing of the RBCs and counting of the leukocytes electrically using microfabricated platinum electrodes. For RBCs and platelets, 1 μL of whole blood is diluted with PBS on-chip and the cells are counted electrically. The total time for measurement is under 20 minutes. We demonstrate a high correlation of blood cell counts compared to results acquired with a commercial hematology analyzer. This technology could potentially have tremendous applications in hospitals at the bedside, private clinics, retail clinics and the developing world.

Contribution of GLC3A locus to Primary Congenital Glaucoma in Pakistani population

OBJECTIVES

To check the contribution of GLC3A locus to primary congenital glaucoma in the Pakistani population.

METHODS

We enrolled twenty-nine sporadic cases and three families with multiple individuals affected with recessive primary congenital glaucoma in the year 2013. It was a genetic linkage study accomplished jointly in Department of Biotechnology of Lahore College for Women University and School of Biological Sciences, University of the Punjab, Lahore. Samples from all affected individuals were checked for homozygosity for alleles of microsatellite markers spanning CYP1B1 at GLC3A locus. Genotyping was performed with fluorescently labeled primers by capillary electrophoresis. For familial cases, linkage was evaluated by checking the co-segregation of the phenotype with the genotypes. Two-point LOD score was calculated for each microsatellite marker with MLINK.

RESULTS

Our study revealed that GLCA3 may contribute to glaucoma in 17% of the sporadic cases and patients in 2 of the 3 families.

CONCLUSIONS

This data suggests that the GLC3A may make an important contribution to autosomal recessive primary congenital glaucoma in the Pakistani population. Genotyping and Sequencing of more families will be helpful to identify the common mutations in CYP1B1 in future.

Mutations of GJB2 encoding connexin 26 contribute to non-syndromic moderate and severe hearing loss in Pakistan

Mutations of GJB2 which encode connexin 26, contribute to 6-7 % of profound deafness in Pakistan. We investigated the involvement of GJB2 mutations in a cohort of 84 pedigrees and 86 sporadic individuals with moderate or severe hearing loss. Individuals in eight consanguineous families and four sporadic cases (9.52 and 4.65 %, respectively) were homozygous or compound heterozygous for p.W24X or p.W77X mutations in GJB2. These two variants are also among the most common mutations known to cause profound deafness in South Asia. The association of identical mutations with both profound and less severe phenotype of hearing loss suggests that alleles of other genes modify the phenotype due to these GJB2 nonsense mutations. Our study demonstrates that GJB2 mutations are an important contributor to aetiology of moderate to severe hearing loss in Pakistan.

Coincidence detection of heterogeneous cell populations from whole blood with coplanar electrodes in a microfluidic impedance cytometer

Particle counting finds many industrial applications especially in medical healthcare. In particular, cell counting from whole blood is used pervasively for disease diagnostics. Microfluidic impedance cytometry is fast, requires a small volume of blood, can be used at point of care and can perform absolute enumeration of different cell types in the sample. Coincidence detection is very essential for accurate counting results and becomes more significant while counting specific target cells, e.g. CD4(+) or CD8(+) T cell count in HIV/AIDS patient blood samples. In heterogeneous samples, e.g. blood, cell differentiation for all coincidence occurrences is essential in addition to the coincidence detection for accurate cell enumeration. In this paper, we have characterized the coincidence detection with cell differentiation using a microfluidic impedance biochip. The pure population of leukocytes is obtained after all erythrocytes are lysed on-chip from whole blood. Leukocytes were counted electrically as they pass over coplanar microfabricated electrodes bonded to the 15 μm × 15 μm cross section counting channel while generating a bipolar pulse for each cell passage. We have developed a mathematical model to simulate the electrical cell pulse and its coincidences. We show that coincidence detection can be characterized into three main types based on the range of time delay at which the coincidence occurs. We have also characterized cell differentiation for all the three coincidence types and show that multiple coincidences of different types can also occur. We used healthy and HIV-infected patient blood samples and used our coincidence detection technique to count CD4(+) and CD8(+) T cells and show the improvement in accuracy of cell counts compared to that without coincidence detection. We have also shown the improvement in the erythrocyte counting with coincidence detection in diluted whole blood samples.

Evaluation of antioxidant and antimicrobial potential of two endangered plant species Atropa belladonna and Matricaria chamomilla

BACKGROUND

Plants are the natural source of antioxidants as well as antimicrobial compounds that has great potentials in pharmaceutical industry. In the present study, two medicinal plants Atropa belladonna and Matricaria chamomilla were collected from Northern areas of Pakistan.

MATERIALS AND METHODS

The extracts of the collected plants were obtained by microwave assisted extraction (MAE) with changing parameters, power level and time; methanol and ethanol were solvents used during extraction. The extracts of plants were tested against different bacterial strains.

RESULTS

It was observed that ethanolic extracts of Atropa belladonna has more significant antimicrobial activity against S.aureus than E.coli. In parallel, methanolic extract of Matricaria chamomilla showed greater significant antibacterial activity against S.aureus when compared with E.coli. In comparison, ethanolic extracts of Matricaria chamomilla has shown more significant results against S. aureus than E.coli (p ≤ 0.05). Both plants had no antibacterial activity against S.typhi. The free radical scavenging activity observed by DPPH assay, indicate that both plants have antioxidant activity at all levels of concentrations in solvent tested during the present work. However, methanolic extracts had greater antioxidant activity when compared with ethanolic extracts.

CONCLUSION

Present study is thus helpful in highlighting present potentials for antioxidant and antimicrobial properties in the selected plants.

Dysferlin regulates cell membrane repair by facilitating injury-triggered acid sphingomyelinase secretion

Dysferlin deficiency compromises the repair of injured muscle, but the underlying cellular mechanism remains elusive. To study this phenomenon, we have developed mouse and human myoblast models for dysferlinopathy. These dysferlinopathic myoblasts undergo normal differentiation but have a deficit in their ability to repair focal injury to their cell membrane. Imaging cells undergoing repair showed that dysferlin-deficit decreased the number of lysosomes present at the cell membrane, resulting in a delay and reduction in injury-triggered lysosomal exocytosis. We find repair of injured cells does not involve formation of intracellular membrane patch through lysosome-lysosome fusion; instead, individual lysosomes fuse with the injured cell membrane, releasing acid sphingomyelinase (ASM). ASM secretion was reduced in injured dysferlinopathic cells, and acute treatment with sphingomyelinase restored the repair ability of dysferlinopathic myoblasts and myofibers. Our results provide the mechanism for dysferlin-mediated repair of skeletal muscle sarcolemma and identify ASM as a potential therapy for dysferlinopathy.

Flow metering characterization within an electrical cell counting microfluidic device

Microfluidic devices based on the Coulter principle require a small aperture for cell counting. For applications using such cell counting devices, the volume of the sample also needs to be metered to determine the absolute cell count in a specific volume. Hence, integrated methods to characterize and meter the volume of a fluid are required in these microfluidic devices. Here, we present fluid flow characterization and electrically-based sample metering results of blood through a measurement channel with a cross-section of 15 μm × 15 μm (i.e. the Coulter aperture). Red blood cells in whole blood are lysed and the remaining fluid, consisting of leukocytes, erythrocyte cell lysate and various reagents, is flown at different flow rates through the measurement aperture. The change in impedance across the electrodes embedded in the counting channel shows a linear relationship with the increase in the fluid flow rate. We also show that the fluid volume can be determined by measuring the decrease in pulse width, and increase in number of cells as they pass through the counting channel per unit time.

3D fabrication of biological machines

Cell-based biological machines can be defined as a set of sub-components consisting of living cells and cell-instructive micro-environments that interact to perform a range of prescribed tasks. The realization of biological machines and their sub-components will require a number of suitable cell sources, biomaterials, and enabling technologies. Here, we review our group's recent accomplishments and continuing efforts toward the development of building biological machines.

The c.42_52del11 mutation in TPRN and progressive hearing loss in a family from Pakistan

The DFNB79 locus harbors TPRN mutations in which have been reported in a few families with deafness. Four frameshift mutations in TPRN have been described to cause severe or severe-to-profound hearing loss in Moroccan and Pakistani families, and a single frameshift mutation was associated with progressive hearing loss in deaf individuals in a Dutch family. We identified a Pakistani family in which the affected individuals were homozygous for a pathogenic mutation, c.42_52del11, in TPRN (p.G15Afs150X). In contrast to the previously reported individuals affected by the same mutation, hearing loss is likely to be progressive in this family. Thus the same mutation of TPRN can be associated with different thresholds of hearing as well as differences in the stability of the phenotype.

SLC26A4 mutations in patients with moderate to severe hearing loss

Mutations in SLC26A4 cause either syndromic or nonsyndromic hearing loss. We identified a link between hearing loss and DFNB4 in 3 of the 50 families participating in this study. Sequencing analysis revealed two SLC26A4 mutations, p.V239D and p.S57X, in affected members of the 3 families. These mutations have been previously reported in deaf individuals from the subcontinent, all of whom manifested profound deafness. The patients investigated in our study exhibited moderate to severe hearing loss. Our results show that inactivating SLC26A4 mutations that cause profound deafness can also be involved in the etiology of moderate to severe hearing loss. The type of mutation cannot predict the severity of the hearing loss in all cases, and there may be additional epistatic interactions that could modify the phenotype.

Electrical flow metering of blood for point-of-care diagnostics

We have developed a microfabricated chip that creates a purified white blood cell (WBC) population from whole blood samples and then electrically analyzes the WBCs at the same time as measuring sample volume flown. The flow metering is based on the measurement of the electrical admittance between microelectrodes inside a microfluidic channel. We found that the admittance related to the flow rate linearly. WBC counts which correlated with the flow rate shows how this technique is a viable method in metering and analyzing blood and other biological samples in a point-of-care environment.

Prioritized sequencing of the second exon of MYO15A reveals a new mutation segregating in a Pakistani family with moderate to severe hearing loss

Mutations in MYO15A are associated with deafness in humans, and shaker 2 mice also exhibit a hearing loss due to defects of unconventional myosin 15a. We ascertained a consanguineous Pakistani family with recessively inherited moderate to severe hearing loss, which putatively segregated with markers linked to the DFNB3 locus. Prioritized sequencing of the second exon of MYO15A from the DNA of all affected individuals of family revealed a duplication of Cytosine in a stretch of seven repetitive C nucleotides (c.1185dupC). This mutation results in a frameshift and incorporates a stop codon in the open reading frame of MYO15A (p.E396fsX431). The findings of less severe hearing loss in families with linkage to DFNB3 are only reported for some individuals with mutations in exon 2 of MYO15A, which are further supported by this study. Therefore, on basis of linkage data and the presence of a less severe hearing loss phenotype, sequencing of a single exon of MYO15A can efficiently identify the causative mutations in patients from these families.

From BioMEMS to Bionanotechnology: Integrated BioChips for the Detection of Cells and Microorganisms

This paper reviews the interdisciplinary work performed in our group in recent years to develop micro-integrated devices to characterize biological entities. We present the use of electrical and mechanically based phenomena to perform characterization and various functions needed for integrated biochips. One sub-system takes advantage of the dielectrophoretic effect to sort and concentrate cells within a micro-fluidic biochip. Another sub-system measures impedance changes produced by the metabolic activity of cells to determine their viability. A third sub-system is used to detect the mass of bacteria as they bind to micro-mechanical silicon cantilevers. These devices with an electronic signal output can be very useful in producing practical systems for rapid detection and characterization of cells for a wide variety of applications in the food safety and health diagnostics industries.

Mutations in CLDN14 are associated with different hearing thresholds

Mutations in CLDN14, encoding tight junction protein claudin 14, cause profound deafness in mice and humans. We identified a Pakistani family, in which the affected individuals were homozygous for a known pathogenic mutation c.254 T>A resulting in p.V85D substitution in CLDN14; however, in contrast to the previously reported families with mutations in CLDN14, most of the affected individuals in this family exhibit only a severe hearing loss. In order to identify the contribution of CLDN14 to less than profound deafness, we screened for mutations of CLDN14 in 30 multiplex and 57 sporadic cases with moderately severe to severe hearing loss from Pakistan. We identified one other affected individual homozygous for p.V85D substitution. Comparison of audiometric data from all patients indicates that mutations in CLND14 cause varying degrees of hearing loss, which may be enhanced at high frequencies. This suggests that a modifier can reduce the severity of hearing loss associated with mutations of CLDN14. Our data indicates that mutations in CLDN14 should be explored when considering the etiology of less severe hearing loss.

A nanoscale Ti∕GaAs metal-semiconductor hybrid sensor for room temperature light detection

We report an individually addressable Ti∕GaAs metal-semiconductor hybrid optical nanosensor with positive photoresistance and a sensitivity that increases as the device dimensions shrink. The underlying physics relates to the crossover from ballistic to diffusive transport of the photoinduced carriers and the geometric enhancement of the effect associated with a Schottky-barrier-coupled parallel metal shunt layer. For a 250 nm device under 633 nm illumination we observe a specific detectivity of D(*)=5.06×10(11) cm √Hz∕W with a dynamic response of 40 dB.

DNA Sensing using Nano-crystalline Surface Enhanced Al(2)O(3) Nanopore Sensors

A new solid-state, Al(2)O(3) nanopore sensor with enhanced surface properties for the real-time detection and analysis of individual DNA molecules is reported. Nanopore formation using electron beam based decomposition transformed the local nanostructure and morphology of the pore from an amorphous, stoichiometric structure (O to Al ratio of 1.5) to a hetero-phase crystalline network, deficient in O (O to Al ratio of ~0.6). Direct metallization of the pore region was observed during irradiation, thereby permitting the potential fabrication of nano-scale metallic contacts in the pore region with potential application to nanopore-based DNA sequencing. Dose dependent phase transformations to purely γ and/or α-phase nanocrystallites were also observed during pore formation allowing for surface charge engineering at the nanopore/fluid interface. DNA transport studies revealed an order of magnitude reduction in translocation velocities relative to alternate solid-state architectures, accredited to high surface charge density and the nucleation of charged nanocrystalline domains. The unique surface properties of Al(2)O(3) nanopore sensors makes them ideal for the detection and analysis of ssDNA, dsDNA, RNA secondary structures and small proteins. These nano-scale sensors may also serve as a useful tool in studying the mechanisms driving biological processes including DNA-protein interactions and enzyme activity at the single molecule level.