Identification and characterization of nuclear localization signals in the circumsporozoite protein of Plasmodium falciparum

Secretory proteins of Plasmodium exhibit differential spatial and functional activity within the host cell nucleus. However, the nuclear localization signals (NLSs) for these proteins remain largely uncharacterized. In this study, we have identified and characterized two NLSs in the circumsporozoite protein of Plasmodium falciparum (Pf-CSP). Both NLSs in the Pf-CSP contain clusters of lysine and arginine residues essential for specific interactions with the conserved tryptophan and asparagine residues of importin-α, facilitating nuclear translocation of Pf-CSP. While the two NLSs of Pf-CSP function independently and are both crucial for nuclear localization, a single NLS of Pf-CSP leads to weak nuclear localization. These findings shed light on the mechanism of nuclear penetrability of secretory proteins of Plasmodium proteins.

Assessing type I collagen expression and quality in cellular models of osteogenesis imperfecta

Osteogenesis imperfecta (OI) is a group of genetic disorders of bone formation characterized by soft and shorter brittle bones in affected individuals. OI is generally considered a collagenopathy resulting from abnormal expression of type I collagen. As assay system to detect the cellular level and quality of type I collagen would help in rapid and correct detection of OI from the diagnostic perspectives. Here, we report an immunofluorescence assay for detection of type I collagen in fibroblast models of OI and represented them into two broad categories based on the expression level and aggregation characteristics of pro-α1(I). Cell phenotypic assays of pro-α1(I) in OI-related gene knocked down fibroblasts revealed aggregates of pro-α1(I) in conditions with knockdown of SERPINF1, CRTAP, P3H1, PPIB, SERPINH1, FKBP10, TMEM38B, MESD, and KDELR2, whereas pro-α1(I) expression was very low in fibroblasts which had knockdown of IFITM5, SP7, BMP1, WNT1, CREB3L1, MBTPS2, and CCDC134. The expression of pro-α1(I) showed abundant and non-aggregated distribution in the fibroblasts with knockdown of non-OI skeletal disorder-related genes (RAB33B and IFT52). The in vitro assay accurately detected abnormally expressed pro-α1(I) levels in cellular models of various types of OI. Thus, this procedure represents a promising point-of-detection assay for potential diagnosis and therapeutic decisions in OI.

The emerging functions of intraflagellar transport 52 in ciliary transport and ciliopathies

Ciliary transport in eukaryotic cells is an intricate and conserved process involving the coordinated assembly and functioning of a multiprotein intraflagellar transport (IFT) complex. Among the various IFT proteins, intraflagellar transport 52 (IFT52) plays a crucial role in ciliary transport and is implicated in various ciliopathies. IFT52 is a core component of the IFT-B complex that facilitates movement of cargoes along the ciliary axoneme. Stable binding of the IFT-B1 and IFT-B2 subcomplexes by IFT52 in the IFT-B complex regulates recycling of ciliary components and maintenance of ciliary functions such as signal transduction and molecular movement. Mutations in the IFT52 gene can disrupt ciliary trafficking, resulting in dysfunctional cilia and affecting cellular processes in ciliopathies. Such ciliopathies caused by IFT52 mutations exhibit a wide range of clinical features, including skeletal developmental abnormalities, retinal degeneration, respiratory failure and neurological abnormalities in affected individuals. Therefore, IFT52 serves as a promising biomarker for the diagnosis of various ciliopathies, including short-rib thoracic dysplasia 16 with or without polydactyly. Here, we provide an overview of the IFT52-mediated molecular mechanisms underlying ciliary transport and describe the IFT52 mutations that cause different disorders associated with cilia dysfunction.

Implementation of Exome Sequencing to Identify Rare Genetic Diseases

Modern high-throughput genomic testing using next-generation sequencing (NGS) has led to a significant increase in the successful diagnosis of rare genetic disorders. Recent advances in NGS tools and techniques have led to accurate and timely diagnosis of a large proportion of genetic diseases by finding sequence variations in clinical samples. One of the NGS techniques, exome sequencing (ES), is considered as a powerful and easily approachable method for genetic disorders in terms of rapid and cost-effective diagnostic yields. In this chapter, we describe an overview of whole exome sequencing (ES) in the context of experimental and analytical methodologies. Approaches to ES include sequencing capture technique, quality control processes at various stages of sequencing analysis, exome data filtering strategy that incorporates both primary and secondary filtering, and prioritization of candidate variants in diagnosing genetic diseases.

Nuclear proteostasis imbalance in laminopathy-associated premature aging diseases

Laminopathies are a group of rare genetic disorders with heterogeneous clinical phenotypes such as premature aging, cardiomyopathy, lipodystrophy, muscular dystrophy, microcephaly, epilepsy, and so on. The cellular phenomena associated with laminopathy invariably show disruption of nucleoskeleton of lamina due to deregulated expression, localization, function, and interaction of mutant lamin proteins. Impaired spatial and temporal tethering of lamin proteins to the lamina or nucleoplasmic aggregation of lamins are the primary molecular events that can trigger nuclear proteotoxicity by modulating differential protein-protein interactions, sequestering quality control proteins, and initiating a cascade of abnormal post-translational modifications. Clearly, laminopathic cells exhibit moderate to high nuclear proteotoxicity, raising the question of whether an imbalance in nuclear proteostasis is involved in laminopathic diseases, particularly in diseases of early aging such as HGPS and laminopathy-associated premature aging. Here, we review nuclear proteostasis and its deregulation in the context of lamin proteins and laminopathies.

Deep intronic mutation in CRTAP results in unstable isoforms of the protein to induce type I collagen aggregation in a lethal type of osteogenesis imperfecta type VII

Genetic mutations are involved in Mendelian disorders. Unbuffered intronic mutations in gene variants can generate aberrant splice sites in mutant transcripts, resulting in mutant isoforms of proteins with modulated expression, stability, and function in diseased cells. Here, we identify a deep intronic variant, c.794_1403A>G, in CRTAP by genome sequencing of a male fetus with osteogenesis imperfecta (OI) type VII. The mutation introduces cryptic splice sites in intron-3 of CRTAP, resulting in two mature mutant transcripts with cryptic exons. While transcript-1 translates to a truncated isoform (277 amino acids) with thirteen C-terminal non-wild-type amino acids, transcript-2 translates to a wild-type protein sequence, except that this isoform contains an in-frame fusion of non-wild-type twenty-five amino acids in a tetratricopeptide repeat sequence. Both mutant isoforms of CRTAP are unstable due to the presence of a unique 'GWxxI' degron, which finally leads to loss of proline hydroxylation and aggregation of type I collagen. Although type I collagen aggregates undergo autophagy, the overall proteotoxicity resulted in death of the proband cells by senescence. In summary, we present a genetic disease pathomechanism by linking a novel deep intronic mutation in CRTAP to unstable mutant isoforms of the protein in lethal OI type VII.

Genome sequencing identifies a large non-coding region deletion of SNX10 causing autosomal recessive osteopetrosis

Autosomal recessive osteopetrosis (ARO) is a rare genetic disorder caused by impaired osteoclast activity. In this study, we describe a 4-year-old boy with increased bone density due to osteopetrosis, autosomal recessive 8. Using genome sequencing, we identified a large deletion in the 5'-untranslated region (UTR) of SNX10 (sorting nexin 10), where the regulatory region of this gene is located. This large deletion resulted in the absence of the SNX10 transcript and led to abnormal osteoclast activity. SNX10 is one of the nine genes known to cause ARO, shown to interact with V-ATPase (vacuolar type H( + )-ATPase), as it plays an important role in bone resorption. Our study highlights the importance of regulatory regions in the 5'-UTR of SNX10 for its expression while also demonstrating the importance of genome sequencing for detecting large deletion of the regulatory region of SNX10.

Mutant MESD links cellular stress to type I collagen aggregation in osteogenesis imperfecta type XX

Aberrant forms of endoplasmic reticulum (ER)-resident chaperones are implicated in loss of protein quality control in rare diseases. Here we report a novel mutation (p.Asp233Asn) in the ER retention signal of MESD by whole exome sequencing of an individual diagnosed with osteogenesis imperfecta (OI) type XX. While MESDD233N has similar stability and chaperone activity as wild-type MESD, its mislocalization to cytoplasm leads to imbalance of ER proteostasis, resulting in improper folding and aggregation of proteins, including LRP5 and type I collagen. Aggregated LRP5 loses its plasma membrane localization to disrupt the expression of WNT-responsive genes, such as BMP2, BMP4, in proband fibroblasts. We show that MESD is a direct chaperone of pro-α1(I) [COL1A1], and absence of MESDD233N in ER results in cytosolic type I collagen aggregates that remain mostly not secreted. While cytosolic type I collagen aggregates block the intercellular nanotubes, decreased extracellular type I collagen also results in loss of interaction of ITGB1 with type I collagen and weaker attachment of fibroblasts to matrix. Although proband fibroblasts show increased autophagy to degrade the aggregated type I collagen, an overall cellular stress overwhelms the proband fibroblasts. In summary, we present an essential chaperone function of MESD for LRP5 and type I collagen and demonstrating how the D233N mutation in MESD correlates with impaired WNT signaling and proteostasis in OI.

Frequency of Defecation and Form of Stool among General Bangladeshi Population

Data on stool form and defecation frequency which are a prerequisite for defining normal bowel habit are lacking in Bangladesh. This observational cross sectional study was designed to find out defecation frequency and stool form among general population in Bangladesh. This study was performed in the Department of Gastroenterology, Shaheed Suhrawardy Medical College Hospital, Dhaka, Bangladesh from July 2017 to June 2018. Apparently healthy 1090 respondents were evaluated for predominant stool form (Bristol chart) and frequency. Data on demographic and life-style were collected. The study population consisted of 1090 respondents, among them, 65.13% male and 34.87% female and mean age of them was 40.20±12.39 years. Most of the people 874(80.2%) passed stool between 12-14 times per week followed by 111(10.2%) less than 3 stools per week, 95(8.7%) passed more than 14 stools per week and 10(0.9%) between 3-12 stools per week, p<0.001. Most people passed predominantly Bristol type IV stool- 610(56.0%); followed by type III- 274(25.1%). Other stool forms were: type I- 52(4.8%), type II- 59(5.4%), type V- 31(2.8%), type VI- 33(3.0%), type VII- 31(2.8%), p<0.001. In regard to the physical activity, most of the respondents (70.0%) are physically active whereas about 13.0% are sedentary and about 17.0% are physically intermediate between the two, p<0.001. In the case of dietary habit, most of the participants are non-vegetarian (82.5%) and the remaining are vegetarian (11.1%) and occasional non vegetarian (6.4%), p<0.001. Median stool frequency in the studied population was 14 per week and predominant form was Bristol type IV. Older age was associated with lesser stool frequency, particularly among female subjects.

The E262K mutation in Lamin A links nuclear proteostasis imbalance to laminopathy-associated premature aging

Deleterious, mostly de novo, mutations in the lamin A (LMNA) gene cause spatio-functional nuclear abnormalities that result in several laminopathy-associated progeroid conditions. In this study, exome sequencing in a sixteen-year-old male with manifestations of premature aging led to the identification of a mutation, c.784G>A, in LMNA, resulting in a missense protein variant, p.Glu262Lys (E262K), that aggregates in nucleoplasm. While bioinformatic analyses reveal the instability and pathogenicity of LMNAE262K , local unfolding of the mutation-harboring helical region drives the structural collapse of LMNAE262K into aggregates. The E262K mutation also disrupts SUMOylation of lysine residues by preventing UBE2I binding to LMNAE262K , thereby reducing LMNAE262K degradation, aggregated LMNAE262K sequesters nuclear chaperones, proteasomal proteins, and DNA repair proteins. Consequently, aggregates of LMNAE262K disrupt nuclear proteostasis and DNA repair response. Thus, we report a structure-function association of mutant LMNAE262K with toxicity, which is consistent with the concept that loss of nuclear proteostasis causes early aging in laminopathies.

Acyl-CoA binding protein regulates nutrient-dependent autophagy

BACKGROUND

Homeostasis of autophagy under normal conditions and nutrient stress is maintained by adaptive activation of regulatory proteins. However, the protein-lipid crosstalk that modulates the switch from suppression to activation of autophagy initiation is largely unknown.

RESULTS

Here, we show that human diazepam-binding inhibitor (DBI), also known as acyl-CoA binding protein (ACBP), binds to phosphatidylethanolamine of the phagophore membrane under nutrient-rich growth conditions, leading to inhibition of LC3 lipidation and suppression of autophagy initiation. Specific residues, including the conserved tyrosine residues of DBI, interact with phosphatidylethanolamine to stabilize the later molecule in the acyl-CoA binding cavity of the protein. Under starvation, phosphorylation of serine-21 of DBI mediated by the AMP-activated protein kinase results in a drastic reduction in the affinity of the protein for phosphatidylethanolamine. The release of serine-21 phosphorylated DBI from the phagophore upon nutrient starvation restores the high LC3 lipidation flux and maturation of the phagophore to autophagosome.

CONCLUSION

DBI acts as a strategic barrier against overactivation of phagophore maturation under nutrient-rich conditions, while triggering autophagy under nutrient-deficient conditions.

HYPK coordinates degradation of polyneddylated proteins by autophagy

Selective degradation of protein aggregates by macroautophagy/autophagy is an essential homeostatic process of safeguarding cells from the effects of proteotoxicity. Among the ubiquitin-like proteins, NEDD8 conjugation to misfolded proteins is prominent in stress-induced protein aggregates, albeit the function of neddylation in autophagy is unclear. Here, we report that polyneddylation functions as a post-translational modification for autophagic degradation of proteotoxic-stress induced protein aggregates. We also show that HYPK functions as an autophagy receptor in the polyneddylation-dependent aggrephagy. The scaffolding function of HYPK is facilitated by its C-terminal ubiquitin-associated domain and N-terminal tyrosine-type LC3-interacting region which bind to NEDD8 and LC3 respectively. Both NEDD8 and HYPK are positive modulators of basal and proteotoxicity-induced autophagy, leading to protection of cells from protein aggregates, such as aggregates of mutant HTT exon 1. Thus, we propose an indispensable and additive role of neddylation and HYPK in clearance of protein aggregates by autophagy, resulting in cytoprotective effect during proteotoxic stress.Abbreviations: ATG5, autophagy related 5; ATG12, autophagy related 12; ATG14, autophagy related 14; BECN1, beclin 1; CBL, casitas B-lineage lymphoma; CBLB, Cbl proto-oncogene B; GABARAP, GABA type A receptor-associated protein; GABARAPL1, GABA type A receptor associated protein like 1; GABARAPL2, GABA type A receptor associated protein like 2; GFP, green fluorescent protein; HTT, huntingtin; HTT97Q exon 1, huntingtin 97-glutamine exon 1; HUWE1, HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1; HYPK, huntingtin interacting protein K; IgG, immunoglobulin G; IMR-32, Institute for Medical Research-32; KD, knockdown; K_d, dissociation constant; LAMP1, lysosomal associated membrane protein 1; LIR, LC3 interacting region; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MAP1LC3A/LC3A, microtubule associated protein 1 light chain 3 alpha; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; MARK1, microtubule affinity regulating kinase 1; MARK2, microtubule affinity regulating kinase 2; MARK3, microtubule affinity regulating kinase 3; MARK4, microtubule affinity regulating kinase 4; MCF7, Michigan Cancer Foundation-7; MTOR, mechanistic target of rapamycin kinase; NAE1, NEDD8 activating enzyme E1 subunit 1; NBR1, NBR1 autophagy cargo receptor; NEDD8, NEDD8 ubiquitin like modifier; Ni-NTA, nickel-nitrilotriacetic acid; NUB1, negative regulator of ubiquitin like proteins 1; PIK3C3, phosphatidylinositol 3-kinase catalytic subunit type 3; PolyQ, poly-glutamine; PSMD8, proteasome 26S subunit, non-ATPase 8; RAD23A, RAD23 homolog A, nucleotide excision repair protein; RAD23B, RAD23 homolog B, nucleotide excision repair protein; RFP, red fluorescent protein; RPS27A, ribosomal protein S27a; RSC1A1, regulator of solute carriers 1; SNCA, synuclein alpha; SIK1, salt inducible kinase 1; siRNA, small interfering ribonucleic acid; SOD1, superoxide dismutase 1; SPR, surface plasmon resonance; SQSTM1, sequestosome 1; SUMO1, small ubiquitin like modifier 1; TAX1BP1, Tax1 binding protein 1; TDRD3, tudor domain containing 3; TNRC6C, trinucleotide repeat containing adaptor 6C; TOLLIP, toll interacting protein; TUBA, tubulin alpha; TUBB, tubulin beta class I; UBA, ubiquitin-associated; UBA1, ubiquitin like modifier activating enzyme 1; UBA5, ubiquitin like modifier activating enzyme 5; UBAC1, UBA domain containing 1; UBAC2, UBA domain containing 2; UBAP1, ubiquitin associated protein 1; UBAP2, ubiquitin associated protein 2; UBASH3B, ubiquitin associated and SH3 domain containing B; UBD/FAT10, ubiquitin D; UBE2K, ubiquitin conjugating enzyme E2 K; UBLs, ubiquitin-like proteins; UBL7, ubiquitin like 7; UBQLN1, ubiquilin 1; UBQLN2, ubiquilin 2; UBQLN3, ubiquilin 3; UBQLN4, ubiquilin 4; UBXN1, UBX domain protein 1; ULK1, unc-51 like autophagy activating kinase 1; URM1, ubiquitin related modifier 1; USP5, ubiquitin specific peptidase 5; USP13, ubiquitin specific peptidase 13; VPS13D, vacuolar protein sorting 13 homolog D.

Pairwise Balanced Designs From Cyclic PBIB Designs

A pairwise balanced designs was constructed using cyclic partially balanced incomplete block designs with either (λ1 – λ2) = 1 or (λ2 – λ1) = 1. This method of construction of Pairwise balanced designs is further generalized to construct it using cyclic partially balanced incomplete block design when |(λ1 – λ2)| = p. The methods of construction of pairwise balanced designs was supported with examples. A table consisting parameters of Cyclic PBIB designs and its corresponding constructed pairwise balanced design is also included.

Differential Stabilities of Mefloquine-Bound Human and Plasmodium falciparum Acyl-CoA-Binding Proteins

Toxic effects of pharmacological drugs restrict their robust application against human diseases. Although used as a drug in the combinatorial therapy to treat malaria, the use of mefloquine is not highly recommended because of its adverse effects in humans. Mefloquine inhibits the binding of acyl-CoAs to acyl-CoA-binding proteins of Plasmodium falciparum (PfACBPs) and human (hACBP). In this study, we have used molecular dynamics simulation and other computational approaches to investigate the differences of stabilities of mefloquine-PfACBP749 and mefloquine-hACBP complexes. The stability of mefloquine in the binding cavity of PfACBP749 is less than its stability in the binding pocket of hACBP. Although the essential tyrosine residues (tyrosine-30 and tyrosine-33 of PfACBP749 and tyrosine-29 and tyrosine-32 of hACBP) mediate the initial binding of mefloquine to the proteins by π-stacking interactions, additional temporally longer interactions between mefloquine and aspartate-22 and methionine-25 of hACBP result in stronger binding of mefloquine to hACBP. The higher fluctuation of mefloquine-binding residues of PfACBP749 contributes to the instability of mefloquine in the binding cavity of the protein. On the contrary, in the mefloquine-bound state, the stability of hACBP protein is less than the stability of PfACBP749. The helix-to-coil transition of the N-terminal hydrophobic region of hACBP has a destabilizing effect upon the protein's structure. This causes the induction of aggregation properties in the hACBP in the mefloquine-bound state. Taken together, we describe the mechanistic features that affect the differential dynamic stabilities of mefloquine-bound PfACBP749 and hACBP proteins.

The metastable states of proteins

The intriguing process of protein folding comprises discrete steps that stabilize the protein molecules in different conformations. The metastable state of protein is represented by specific conformational characteristics, which place the protein in a local free energy minimum state of the energy landscape. The native-to-metastable structural transitions are governed by transient or long-lived thermodynamic and kinetic fluctuations of the intrinsic interactions of the protein molecules. Depiction of the structural and functional properties of metastable proteins is not only required to understand the complexity of folding patterns but also to comprehend the mechanisms of anomalous aggregation of different proteins. In this article, we review the properties of metastable proteins in context of their stability and capability of undergoing atypical aggregation in physiological conditions.

Mefloquine binding to human acyl-CoA binding protein leads to redox stress-mediated apoptotic death of human neuroblastoma cells

Malaria is an infectious disease that is caused by different species of Plasmodium. Several antimalarial drugs are used to counter the spread and infectivity of Plasmodium species. However, humans are also vulnerable to many of the antimalarial drugs, including the quinoline-based drugs. In particular, the antimalarial mefloquine has been reported to show adverse neuropsychiatric effects in humans. Though mefloquine is known to be neurotoxic, the molecular mechanisms associated with this phenomenon are still obscure. In this study, we show that mefloquine binds to and inactivates the human acyl-CoA binding protein (hACBP), potentially inducing redox stress in human neuroblastoma cells (IMR-32). Mefloquine occupies the acyl-CoA binding pocket of hACBP by interacting with several of the critical acyl-CoA binding amino acids. This leads to the competitive inhibition of acyl-CoA(s) binding to hACBP and to the accumulation of lipid droplets inside the IMR-32 cells. The accumulation of cytosolic lipid globules and oxidative stress finally correlates with the apoptotic death of cells. Taken together, our study deciphers a mechanistic detail of how mefloquine leads to the death of human cells by perturbing the activity of hACBP and lipid homeostasis.

T54R mutation destabilizes the dimer of superoxide dismutase 1T54R by inducing steric clashes at the dimer interface

Mutations cause abnormalities in protein structure, function and oligomerization. Different mutations in the superoxide dismutase 1 (SOD1) protein cause its misfolding, loss of dimerization and aggravate its aggregation in the amyotrophic lateral sclerosis disease. In this study, we report the mechanistic details of how a threonine-to-arginine mutation at the 54^th position (T54R) of SOD1 results in destabilization of the dimer interface of SOD1^T54R. Using computational and experimental methods, we show that the T54R mutation increases fluctuation of the mutation-harboring loop (R54-loop) of SOD1^T54R. Fluctuation of this loop causes steric clashes that involve arginine-54 (R54) and other residues of SOD1^T54R, resulting in loss of inter-subunit contacts at the dimer interface. Since the T54 residue-containing loop is necessary for the dimerization of wild-type SOD1, fluctuation of the R54-loop, steric clashes involving R54 and loss of inter-subunit contacts give rise to the loss of SOD1^T54R dimer stability. This correlates to energetically unfavorable tethering of the monomers of SOD1^T54R. The outcome is gradual splitting of SOD1^T54R dimers into monomers, thereby exposing the previously buried hydrophobic interface residues to the aqueous environment. This event finally leads to aggregation of SOD1^T54R. T54R mutation has no effect in altering the relative positions of copper and zinc ion binding residues of SOD1^T54R. The native SOD1 structure is stable, and there is no destabilizing effect at its dimer interface. Overall, our study reveals the intricate mechanism of T54R mutation-associated destabilization of the dimer of the SOD1^T54R protein.

T54R mutation destabilizes the dimer of SOD1^T54R.

An IRES-dependent translation of HYPK mRNA generates a truncated isoform of the protein that lacks the nuclear localization and functional ability

Different mechanisms of translation initiation process exist to start the protein synthesis from various viral and eukaryotic mRNA. The cap-independent and tertiary structure directed translation initiation of mRNAs forms the basis of internal ribosome entry site (IRES) mediated translation initiation that helps in cellular protein production in different conditions. HYPK protein sequesters different aggregation-prone proteins to help in the cellular proteostasis. HYPK mRNA is differentially translated from an internal start/initiation codon to generate an amino terminal-truncated isoform (HSPC136) of HYPK protein. In this study, we report that an IRES-dependent translation initiation of HYPK mRNA results in the formation of the HSPC136/HYPK-ΔN isoform of HYPK protein. The IRES-driven translation product, HYPK-ΔN, lacks the N-terminal tri-arginine motif that acts as the nuclear localization signal (NLS) in the full-length HYPK protein. While the full-length HYPK protein translocates to the nucleus and prevents the aggregation of the mutant p53 (p53-R248Q) protein, the HYPK-ΔN lacks this activity. The NLS of HYPK is not evolutionarily conserved and its exclusive presence in the HYPK of higher eukaryotic animals imparts additional advantage to the HYPK protein in tackling the cytosolic as well as nuclear protein aggregates. The presence of the NLS in full-length HYPK also allows this protein to modulate the cell cycle. These results provide a mechanistic detail of HYPK mRNA's translation initiation control by an IRES that dictates the formation of HYPC136/HYPK-ΔN which lacks the nuclear localization and functional ability.

Characterization of Lipid Binding Properties of Plasmodium falciparum Acyl-Coenzyme A Binding Proteins and Their Competitive Inhibition by Mefloquine

Malaria remains a worldwide concern in terms of morbidity and mortality. Limited understanding of the Plasmodium proteome makes it challenging to control malaria. Understanding of the expression and functions of different Plasmodium proteins will help in knowing this organism's virulence properties, besides facilitating the drug development process. In this study, we characterize the lipid binding and biophysical properties of the putative Plasmodium falciparum acyl-CoA binding proteins (PfACBPs), which may have intriguing functions in different stages of P. falciparum life cycle. While the PfACBPs can bind to long-chain fatty acyl-CoAs with high affinity, their affinity for short-chain fatty acyl-CoAs is weak. Base-stacking, electrostatic, and hydrophobic interactions between the aromatic rings, charged groups or residues, and hydrophobic chains or residues are responsible for acyl-CoA binding to PfACBPs. PfACBPs can also bind to phospholipids. PfACBPs cannot bind to the fatty acids and unphosphorylated fatty acid esters. PfACBPs are globular-helical proteins that contain a conserved acyl-CoA binding region. They exist in folded or unfolded conformations without attaining any intermediate state. In a systematic high-throughput in silico screening, mefloquine is identified as a potential ligand of PfACBPs. Binding affinities of mefloquine are much higher than those of fatty acyl-CoAs for all PfACBPs. Mefloquine binds to the acyl-CoA binding pocket of PfACBPs, thereby engaging many of the critical residues. Thus, mefloquine acts as a competitive inhibitor against fatty acyl-CoA binding to PfACBPs, leading to the prevention of P. falciparum growth and proliferation. Taken together, our study characterizes the functions of annotated PfACBPs and highlights the mechanistic details of their inactivation by mefloquine.

The ATPase VCP/p97 functions as a disaggregase against toxic Huntingtin-exon1 aggregates

Intracellular protein aggregation is characterized by accumulation of misfolded proteins. Chaperones, degradation machineries, and quality-control mechanisms counteract protein aggregation. In this study, we report that the ATPase valosin-containing protein (VCP/p97) acts as a functional disaggregase that disassembles Huntingtin-exon1 aggregates in vitro and in HeLa cells. The N-terminal part of VCP (Cdc48_N domain) interacts with the N-terminal 17-amino acid region of Huntingtin-exon1. We show that VCP has properties of a disaggregase, since it is capable of reducing preformed protein aggregates and displays increased ATPase activity in the presence of protein aggregates. However, VCP shows high divergence/disparity from other disaggregases. Taken together, our studies show the novel function of VCP/p97 as a disaggregase which detangles protein aggregates to probably channelize their degradation.

Models, Regulations, and Functions of Microtubule Severing by Katanin

Regulation of microtubule dynamics depends on stochastic balance between polymerization and severing process which lead to differential spatiotemporal abundance and distribution of microtubules during cell development, differentiation, and morphogenesis. Microtubule severing by a conserved AAA family protein Katanin has emerged as an important microtubule architecture modulating process in cellular functions like division, migration, shaping and so on. Regulated by several factors, Katanin manifests connective crosstalks in network motifs in regulation of anisotropic severing pattern of microtubule protofilaments in cell type and stage dependent way. Mechanisms of structural disintegration of microtubules by Katanin involve heterogeneous mechanochemical processes and sensitivity of microtubules to Katanin plays significant roles in mitosis/meiosis, neurogenesis, cilia/flagella formation, cell wall development and so on. Deregulated and uncoordinated expression of Katanin has been shown to have implications in pathophysiological conditions. In this paper, we highlight mechanistic models and regulations of microtubule severing by Katanin in context of structure and various functions of Katanin in different organisms.

Serum transaminase level changes in dengue fever and its correlation with disease severity

It was observed that liver enzymes are elevated in dengue fever. In this study our aims were to determine the changes in serum transaminases in dengue fever, dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) and to find out the relation of transaminase level changes with the disease severity. This cross sectional, prospective hospital based observational study was carried out in the department of Gastrointestinal Hepatobiliary and Pancreatic diseases and Internal Medicine department of BIRDEM Hospital, Dhaka. Patients are classified into 3 groups depending on clinical & laboratory findings: Group 1 dengue fever (DF), Group 2 dengue hemorrhagic fever & Group 3 dengue shock syndrome. A total of 240 cases were taken in this study who fulfilled the selection criteria. Out of whom 125 male and 115 female patients. DF was 157(65.4%) & DHF was 83(34.6%). Aminotransferases [aspartate aminotransferase (AST) and alanine aminotransferase (ALT)] were significantly raised in DHF cases compared to those of classical dengue fever (AST 84.5±42.4 in DF vs. 507±106.8 IU/L in DHF and ALT 59.9±31.3 in DF vs. 234±30.6 IU/L in DHF). The rise of AST is far greater than ALT in both DF and DHF. Dengue fever is usually associated with mild to moderate elevations of aminotransferase levels. The increase in aminotransferases, mainly AST has been associated with disease severity and serves as an early indicator of dengue infection.

Multi-frequency EPR and Mössbauer spectroscopic studies on freeze-quenched reaction intermediates of nitric oxide synthase

It is believed by analogy to chloroperoxidase (CPO) from Caldariomyces fumago that the electronic structure of the intermediate iron-oxo species in the catalytic cycle of nitric oxide synthase (NOS) corresponds to an iron(IV) porphyrin-pi -cation radical. Such species can also be produced by the reaction of ferric NOS with external oxidants within the shunt pathway. We present multi-frequency EPR (9.6, 94, 285 GHz) and Mössbauer spectroscopic studies on freeze-quenched intermediates of the oxygenase domain of nitric oxide synthase which has reacted with peroxy acetic acid within 8-200 ms. The intermediates of the oxygenase domain of both the cytokine inducible NOS (iNOSox) and the neuronal NOS (nNOSox) show an organic radical signal in the 9.6-GHz spectrum overlapping with the spectrum of an unknown species with g-values of 2.24, 2.23 and 1.96. Using 94- and 285-GHz EPR the organic radical signal is assigned to a tyrosine radical on the basis of g-values (i.e. Tyr*562 in nNOSox and Tyr*341 in iNOSox). Mössbauer spectroscopy of (57)Fe-labeled unreacted nNOSox shows a ferric low-spin heme-iron (delta = 0.38 mms(-1), deltaE(Q) = 2.58 mms(-1)). The reaction of nNOSox with peroxy acetic acid for 8 ms leads to the disappearance of the magnetic background characteristic for native nNOSox and a new species with delta = 0.27 mms(-1) and deltaE(Q) = 2.41 mms(-1) is detected at 4.2 K which does not resemble the parameters typical for a Fe(IV) center. It is proposed that this intermediate species corresponds to a ferric low-spin species which magnetically couples to an amino acid radical (presumably Trp*409).

Separation of thoraco-omphalopagus Siamese twin

A pair of female thoraco-omphalopagus twins, with two pairs of lungs, common diaphragm and separate pleural cavities was separated at the age of 5(1/2) months after a parasitic relationship had developed between them. Before separation both the babies developed recurrent respiratory tract infection and frequent diarrhea. They were treated with medical therapy and made fit for anesthesia. The combined weight of the twins was 4(1/2) kg at birth and the combined weight at the time of separation was 9(1/2) kg. One baby was smaller in growth compared to the other baby. The closure of anterior abdominal wall was difficult in both babies. However, we could close it without use of any biodegradable patches or tissue expander. Both the babies survived and are doing well after 3 months of separation.

High pressure fourier transform infrared (FT-IR) spectroscopic studies on inducible nitric oxide (NO) synthase active site: a comparison to cytochrome p450CAM

High pressure Fourier transform infrared (FT-IR) spectroscopy is performed for the first time to analyse the active site of inducible nitric oxide synthase (iNOSox) using the carbon monoxide (CO) heme iron ligand stretch mode (nuCO) as spectroscopic probe. A membrane-driven sapphire anvil high-pressure cell is used. Three major conformational substates exist in substrate-free iNOSox which are characterized by nuCO at approximately 1936, 1945 and 1952 cm(-1). High pressure favors the 1936 cm(-1) substate with a volume difference to the 1945 substate of approximately -21 cm3/mol. The pressure induced cytochrome P420 formation with a reaction volume of approximately -80 cm3/mol is observed. Arginine binding produces a very low nuCO at approximately 1905 cm(-1) caused by the H-bond from the substrate to CO. nuCO for the substates in the substrate-free and arginine-bound proteins shift linearly with pressure which is qualitatively similar to the observation on cytochrome P450cam. The slightly smaller positive slope of the shift in substrate-free iNOSox compared to substrate-free P450cam is interpreted as a slightly lesser compressible heme pocket. In contrast, the significant slower negative slope for arginine-bound iNOSox compared to camphor-bound P450cam results from the different kind of interactions to the CO ligand (electrostatic interaction in P450cam, H-bond in iNOSox).

Particle size distribution and respiratory deposition estimates of beryllium aerosols in an extraction and processing plant

The mass size distribution of beryllium aerosols generated in the various operational areas of a typical extraction and processing plant was studied using an eight-stage impactor sampler. The total concentration of beryllium in the plant was found to be well below the threshold limit value. The mean value of mass median aerodynamic diameter of beryllium particles observed for various operations ranged from 5.0-9.5 microm. The alveolar deposition for various operational areas was estimated to be 3-5% for nasal breathing and 9-13% for oral breathing based on the International Commission on Radiological Protection (ICRP) human respiratory tract model. Deposition during oral breathing was higher than during nasal breathing by approximately a factor of two to three. This study on exposure characterization was useful for reducing the respirable fraction of beryllium aerosol by optimizing the capture velocity and improving the quality of other control measures.

Beryllium: an easily scavenged metal ion in the environment

This study was specifically aimed to determine the levels of beryllium in environmental samples near the vicinity of the beryllium metal plant (BMP). Air particulate samples collected at the BMP site, in the non-monsoon and monsoon seasons, showed an average beryllium concentration of 0.3 and 0.1 ng m(-3) respectively, where as rain water samples showed the beryllium values in the range of 0.01-0.2 ng ml(-1). The suspended particulate matter (dust load) at the site studied was 570 and 250 microg m(-3) in the non-monsoon and monsoon seasons respectively. The results obtained show that, in the environment, 80% of the total beryllium present is removed by rain.

Immobilisation of beryllium in solid waste (red-mud) by fixation and vitrification

The objective of this study was to obtain information on the immobilization of beryllium (Be) in solid waste generated in the extraction process of beryllium from its ore, Beryl. This solid waste, termed red-mud, contains oxides of iron, aluminium, calcium, magnesium and beryllium. The red-mud waste contains beryllium at levels above the permissible limit, which prevents its disposal as solid waste. The total beryllium content in the red-mud analysed showed value ranging from 0.39 to 0.59% Be The studies showed that 50% of the total beryllium in red-mud can be extracted by water by repeated leaching over a period of 45 days. The cement mix, casting into cement blocks, was subjected to leachability studies over a period of 105 days and immobilization factor (IF factor) was determined. These IF values, of the order of 102, were compared with those obtained by performing leachability study on vitrified red-mud masses produced at different temperature conditions. Direct heating of the red-mud gave the gray coloured, non-transparent vitreous mass (as 'bad glass') showed effective immobilisation factor for beryllium in red-mud of the order of 10(4).

Host response to infection: the role of CpG DNA in induction of cyclooxygenase 2 and nitric oxide synthase 2 in murine macrophages

Depending on sequence, bacterial and synthetic DNAs can activate the host immune system and influence the host response to infection. The purpose of this study was to determine the abilities of various phosphorothioate oligonucleotides with cytosine-guanosine-containing motifs (CpG DNA) to activate macrophages to produce nitric oxide (NO) and prostaglandin E(2) (PGE(2)) and to induce expression of NO synthase 2 (NOS2) and cyclooxygenase 2 (COX2). As little as 0.3 microg of CpG DNA/ml increased NO and PGE(2) production in a dose- and time-dependent fashion in cells of the mouse macrophage cell line J774. NO and PGE(2) production was noted by 4 to 8 h after initiation of cultures with the CpG DNA, with the kinetics of NO production induced by CpG DNA being comparable to that induced by a combination of lipopolysaccharide and gamma interferon. CpG DNA-treated J774 cells showed enhanced expression of NOS2 and COX2 proteins as determined by immunoblotting, with the relative potencies of the CpG DNAs generally corresponding to those noted for the induction of NO and PGE(2) production as well as to those noted for the induction of interleukin-6 (IL-6), IL-12, and tumor necrosis factor. Extracts from CpG DNA-treated cells converted L-arginine to L-citrulline, but the NOS inhibitor N(G)-monomethyl-L-arginine (NMMA) inhibited this reaction. The COX2-specific inhibitor NS398 inhibited CpG DNA-induced PGE(2) production and inhibited NO production to various degrees. The NOS inhibitors NMMA, 1400W, and N-iminoethyl-L-lysine effectively blocked NO production and increased the production of PGE(2) in a dose-dependent fashion. Thus, analogues of microbial DNA (i.e., CpG DNA) activate mouse macrophage lineage cells for the expression of NOS2 and COX2, with the production of NO and that of PGE(2) occurring in an interdependent manner.

Characterization of key residues in the subdomain encoded by exons 8 and 9 of human inducible nitric oxide synthase: a critical role for Asp-280 in substrate binding and subunit interactions

Human inducible nitric oxide synthase (iNOS) is active as a dimer of two identical subunits. Each subunit has an amino-terminal oxygenase domain that binds the substrate l-Arg and the cofactors heme and tetrahydrobiopterin and a carboxyl-terminal reductase domain that binds FMN, FAD, and NADPH. We previously demonstrated that a subdomain in the oxygenase domain encoded by exons 8 and 9 is important for dimer formation and NO synthesis. Further, we identified Trp-260, Asn-261, Tyr-267, and Asp-280 as key residues in that subdomain. In this study, using an Escherichia coli expression system, we produced, purified, and characterized wild-type iNOS and iNOS-Ala mutants. Using H(2)O(2)-supported oxidation of N(omega)-hydroxy-l-Arg, we demonstrate that the iNOS mutants' inabilities to synthesize NO are due to selective defects in the oxygenase domain activity. Detailed characterization of the Asp-280-Ala mutant revealed that it retains a functional reductase domain, as measured by its ability to reduce cytochrome c. Gel permeation chromatography confirmed that the Asp-280-Ala mutant exists as a dimer, but, in contrast to wild-type iNOS, urea-generated monomers of the mutant fail to reassociate into dimers when incubated with l-Arg and tetrahydrobiopterin, suggesting inadequate subunit interaction. Spectral analysis reveals that the Asp-280-Ala mutant does not bind l-Arg. This indicates that, in addition to dimerization, proper subunit interaction is required for substrate binding. These data, by defining a critical role for Asp-280 in substrate binding and subunit interactions, give insights into the mechanisms of regulation of iNOS activity.

Beryllium concentrations in ambient air and its source identification. A case study

Beryllium concentrations in atmospheric particulate and soil samples in and around a Beryllium Processing Facility (BPF) have been measured. The mean air concentration level of beryllium in and around the fence line of the BPF is 0.48 +/- 0.43 ng m(-3) (n = 397) and is mostly influenced by diurnal and seasonal changes. The observed air concentration levels were well below the prescribed ambient air quality (AAQ) standard of 10 ng m(-3). The soil concentration levels of beryllium in the study area were found to be in the range of 1.42-2.75 microg g(-1). The mass median aerodynamic diameter (MMAD) of beryllium aerosols in ambient air was found to be 6.9 microm. Source identification using the Enrichment Factor (EF) approach indicates soil as the predominant contributory source for air concentrations at the site.

FT-Infrared spectroscopic studies of the iron ligand CO stretch mode of iNOS oxygenase domain: effect of arginine and tetrahydrobiopterin

The iron ligand CO stretch vibration mode of the inducible nitric oxide synthase oxygenase domain (iNOSox) has been studied from 20 to 298 K. iNOSox in the absence of arginine reveals a temperature-dependent equilibrium of two major conformational substates with CO stretch bands centered at about 1945 and 1954 cm(-)(1). This behavior is not qualitatively changed when tetrahydrobiopterin (H(4)B) is bound. Arginine binding changes significantly the spectrum by formation of a sharp CO stretch mode band at about 1905 cm(-)(1) and indicates the formation of a hydrogen bond to the CO ligand. For temperatures lower than 250 K, the stretch vibration frequency decreases almost linearly with decreasing temperature and indicates that the coupling between the CO ligand and the arginine/protein in the active site via the hydrogen bond is very strong. Flashphotolysis of the CO ligand carried out at 25 K revealed the CO stretch mode of the photodissociated CO ligand trapped in the heme pocket. There is a negative linear relation between the stretch vibration frequencies of the photodissociated and the iron-bound CO indicating that the photodissociated ligand stays near the heme.

N-terminal domain swapping and metal ion binding in nitric oxide synthase dimerization

Nitric oxide synthase oxygenase domains (NOS(ox)) must bind tetrahydrobiopterin and dimerize to be active. New crystallographic structures of inducible NOS(ox) reveal that conformational changes in a switch region (residues 103-111) preceding a pterin-binding segment exchange N-terminal beta-hairpin hooks between subunits of the dimer. N-terminal hooks interact primarily with their own subunits in the 'unswapped' structure, and two switch region cysteines (104 and 109) from each subunit ligate a single zinc ion at the dimer interface. N-terminal hooks rearrange from intra- to intersubunit interactions in the 'swapped structure', and Cys109 forms a self-symmetric disulfide bond across the dimer interface. Subunit association and activity are adversely affected by mutations in the N-terminal hook that disrupt interactions across the dimer interface only in the swapped structure. Residue conservation and electrostatic potential at the NOS(ox) molecular surface suggest likely interfaces outside the switch region for electron transfer from the NOS reductase domain. The correlation between three-dimensional domain swapping of the N-terminal hook and metal ion release with disulfide formation may impact inducible nitric oxide synthase (i)NOS stability and regulation in vivo.

Inducible nitric oxide synthase: role of the N-terminal beta-hairpin hook and pterin-binding segment in dimerization and tetrahydrobiopterin interaction

The oxygenase domain of the inducible nitric oxide synthase (iNOSox; residues 1-498) is a dimer that binds heme, L-arginine and tetrahydrobiopterin (H(4)B) and is the site for nitric oxide synthesis. We examined an N-terminal segment that contains a beta-hairpin hook, a zinc ligation center and part of the H(4)B-binding site for its role in dimerization, catalysis, and H(4)B and substrate interactions. Deletion mutagenesis identified the minimum catalytic core and indicated that an intact N-terminal beta-hairpin hook is essential. Alanine screening mutagenesis of conserved residues in the hook revealed five positions (K82, N83, D92, T93 and H95) where native properties were perturbed. Mutants fell into two classes: (i) incorrigible mutants that disrupt side-chain hydrogen bonds and packing interactions with the iNOSox C-terminus (N83, D92 and H95) and cause permanent defects in homodimer formation, H(4)B binding and activity; and (ii) reformable mutants that destabilize interactions of the residue main chain (K82 and T93) with the C-terminus and cause similar defects that were reversible with high concentrations of H(4)B. Heterodimers comprised of a hook-defective iNOSox mutant subunit and a full-length iNOS subunit were active in almost all cases. This suggests a mechanism whereby N-terminal hooks exchange between subunits in solution to stabilize the dimer.

Occurrence of Witches'-Broom, a New Phytoplasma Disease of Acid Lime (Citrus aurantifolia) in India

In India, acid lime (Citrus aurantifolia (L.) Swingle) is one of the most important citrus fruits grown. It constitutes nearly 20% of the total citrus production. During 1995, an unusual type of disease was observed on a 6-year-old acid lime plant in an orchard in the Nagpur District in eastern Maharashtra. It was named witches'-broom disease (WBD) to reflect the most conspicuous symptom. Other symptoms included small chlorotic leaves, highly proliferated shoots, and shortened internodes. Leaves dropped prematurely and infected twigs were distorted. In advanced stages, infected branches had dieback symptoms. WBD of lime has been reported from Oman and UAE (1) and the causal phytoplasma was designated "Candidatus Phytoplasma aurantifolia" (2). Subsequent surveys in 1995-1998 revealed disease incidences as high as 5% in Maharashtra and in other major acid-lime-growing states-Andhra Pradesh, Tamilnadu, and Karnataka. After the grafting of infected acid lime shoots, disease symptoms developed on Troyer citrange, rough lemon, and Rangpur lime, but not on sweet orange (mosambi), mandarin (Nagpur), or trifoliate orange. The WBD agent was transmitted from infected acid lime to periwinkle (Catharanthus roseus) plants and vice versa by dodder (Cuscuta reflexa). Ultrathin sections of leaf midrib of infected acid lime plants were fixed on copper grids, stained with uranyl acetate and lead acetate, and examined in a JEM 100S transmission electron microscope. Numerous bodies having the characteristic morphology of phytoplasmas were observed in phloem sieve tubes of acid lime in diseased but not in healthy leaves. The phytoplasmal bodies ranged from 100 to 800 nm in diameter and were bounded by a poorly defined membrance. Freehand transverse sections of young internode regions of a WBD-infected periwinkle plant were stained in DAPI (4', 6 diamidino-2-phenylindole; 1.0 μg/ml) and were observed with a fluorescent microscope (Leica). An intense bluish-white fluorescence in the phloem elements of diseased periwinkle and its absence in healthy samples were consistent with the presence of phytoplasmas. This is the first report of phytoplasma-induced witches'-broom disease of acid lime in India. References: (1) M. Garnier et al. Plant Dis. 75:546, 1991. (2) L. Zreik et al. Int. J. Syst. Bacteriol. 45:449,1995.