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- ArticleHatgaonkar A, Hatgoankar K, Jobanputra M, Desale P.Cureus. 2024 Jan;16(1):e51624.Weber's syndrome, named after Hermann Weber, is characterized by midbrain lesions often caused by strokes, resulting in ipsilateral third nerve palsy, including ptosis and pupillary abnormalities, and contralateral hemiplegia. We discuss a case of a 35-year-old lady with cognitive impairment, right hemiparesis, diplopia, left eye ptosis, and lateral eye deviation. MRI of the brain with contrast suggested an acute infarct in the left-sided paramedian region of the midbrain. The oculomotor nucleus and cerebral peduncle were both affected by an abrupt left-sided paramedian midbrain stroke. The participation of particular midbrain nuclei together with symptoms including drooping eyelids, diplopia, and limb paralysis suggested Weber's syndrome. An MRI study of the brain is the modality of choice in suspected stroke cases and is more sensitive when it comes to the brainstem lesions. A comprehensive neurological examination with a clinical diagnosis of Weber's syndrome before radiological investigations is of great help for localizing brain stem lesions and thus aids in early diagnosis and treatment.
- ArticleCohen KR, Anderson D, Ren S, Cook DJ.BMJ Open. 2022 02 25;12(2):e051624.BACKGROUND: The mortality rate of COVID-19 is elevated in males compared with females.
OBJECTIVE: Determine the extent that the elevated thrombotic risk in males relative to females contributes to excess COVID-19 mortality in males.
DESIGN: Observational study.
SETTING: Data sourced from electronic medical records from over 200 US hospital systems.
PARTICIPANTS: 60 877 patients aged 18 years and older hospitalised with COVID-19.
EXPOSURE: Exposure variable: biological sex; key variable of interest: thrombosis.
PRIMARY OUTCOME MEASURES: Primary outcome was COVID-19 mortality. We measured: (1) mortality rate of males relative to females, (2) rate of thrombotic diagnoses occurring during hospitalisation for COVID-19 in both sexes and (3) mortality rate when evidence of thrombosis was present.
RESULTS: The COVID-19 mortality rate of males was 29.9% higher than that of females. Males had a 35.8% higher rate of receiving a thrombotic diagnosis compared with females. The mortality rate of all patients with a thrombotic diagnosis was 40.0%-over twice that of patients with COVID-19 without a thrombotic diagnosis (adjusted OR 2.50 (2.37 to 2.64), p<0.001). When defining thrombosis as either a documented thrombotic diagnosis or a D-dimer level ≥3.0 µg/mL, 16.4% of the excess mortality in male patients could be explained by increased thrombotic risk.
CONCLUSIONS: Our findings suggest the higher COVID-19 mortality rate in males may be significantly accounted for by the elevated risk of thrombosis among males. Understanding the mechanisms that underlie increased male thrombotic risk may allow for the advancement of effective anticoagulation strategies that reduce COVID-19 mortality in males. - ArticleBlom P, Smith GJ, van Kessel MAHJ, Koch H, Lücker S.Microbiol Spectr. 2024 Oct 03;12(10):e0051624.Since the discovery of complete ammonia oxidizers (comammox) within the genus Nitrospira, their distribution and abundance across habitats have been intensively studied to better understand their ecological significance. Many primers targeting their ammonia monooxygenase subunit A gene (amoA) have been designed to detect and quantify comammox bacteria and to describe their community structure. We identified 38 published primers, but only few had high coverage and specificity for all known comammox Nitrospira or one of the two described subclades. For each target group, we comprehensively evaluated selected primer pairs using in silico analyses, endpoint PCRs, qPCRs, and amplicon sequencing on samples from various environments. Endpoint PCRs and qPCRs showed that the most commonly used primer pairs (comaA-244F/659R, comaB-244F/659R, and Ntsp-amoA162F/359R) produced several bands, which likely inflated quantifications via qPCR. In contrast, the recently published primer combinations CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R resulted mostly in a single band. Furthermore, amplicon sequencing demonstrated that these primer combinations also captured the highest richness of comammox Nitrospira. Taken together, our results indicate that few existing comammox amoA primer combinations have both high specificity and coverage and that the choice of these high-specificity and high-coverage primer pairs substantially impacts the accurate detection, quantification, and community description of comammox bacteria. We, therefore, recommend using the CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R primer pairs.IMPORTANCEBacteria that can fully convert ammonia via nitrite to nitrate, the complete ammonia oxidizers (comammox), were recently discovered and are found in many natural and engineered environments. PCR-based tools to study their abundance and diversity were rapidly developed, resulting in a plethora of primers available, many of which are widely used. The presence of comammox bacteria in an environment can, however, only be correctly determined if the used primers detect all members of this group while not detecting any other guilds. This study assesses the coverage and specificity of existing primers targeting comammox bacteria using both computational and standard molecular techniques, revealing large differences in their performance. The uniform usage of well-performing primers across studies could aid in generating comparable and generalizable data to better understand the importance of comammox bacteria in the environment.
- ArticleLarson J, Tokmina-Lukaszewska M, Payne D, Spietz RL, Fausset H, Alam MG, Brekke BK, Pauley J, Hasenoehrl EJ, Shepard EM, Boyd ES, Bothner B.Appl Environ Microbiol. 2024 08 21;90(8):e0051624.Methanogens often inhabit sulfidic environments that favor the precipitation of transition metals such as iron (Fe) as metal sulfides, including mackinawite (FeS) and pyrite (FeS2). These metal sulfides have historically been considered biologically unavailable. Nonetheless, methanogens are commonly cultivated with sulfide (HS-) as a sulfur source, a condition that would be expected to favor metal precipitation and thus limit metal availability. Recent studies have shown that methanogens can access Fe and sulfur (S) from FeS and FeS2 to sustain growth. As such, medium supplied with FeS2 should lead to higher availability of transition metals when compared to medium supplied with HS-. Here, we examined how transition metal availability under sulfidic (i.e., cells provided with HS- as sole S source) versus non-sulfidic (cells provided with FeS2 as sole S source) conditions impact the metalloproteome of Methanosarcina barkeri Fusaro. To achieve this, we employed size exclusion chromatography coupled with inductively coupled plasma mass spectrometry and shotgun proteomics. Significant changes were observed in the composition and abundance of iron, cobalt, nickel, zinc, and molybdenum proteins. Among the differences were alterations in the stoichiometry and abundance of multisubunit protein complexes involved in methanogenesis and electron transport chains. Our data suggest that M. barkeri utilizes the minimal iron-sulfur cluster complex and canonical cysteine biosynthesis proteins when grown on FeS2 but uses the canonical Suf pathway in conjunction with the tRNA-Sep cysteine pathway for iron-sulfur cluster and cysteine biosynthesis under sulfidic growth conditions.IMPORTANCEProteins that catalyze biochemical reactions often require transition metals that can have a high affinity for sulfur, another required element for life. Thus, the availability of metals and sulfur are intertwined and can have large impacts on an organismismal biochemistry. Methanogens often occupy anoxic, sulfide-rich (euxinic) environments that favor the precipitation of transition metals as metal sulfides, thereby creating presumed metal limitation. Recently, several methanogens have been shown to acquire iron and sulfur from pyrite, an abundant iron-sulfide mineral that was traditionally considered to be unavailable to biology. The work presented here provides new insights into the distribution of metalloproteins, and metal uptake of Methanosarcina barkeri Fusaro grown under euxinic or pyritic growth conditions. Thorough characterizations of this methanogen under different metal and sulfur conditions increase our understanding of the influence of metal availability on methanogens, and presumably other anaerobes, that inhabit euxinic environments.
- ArticleOles RE, Carrillo Terrazas M, Loomis LR, Hsu C-Y, Tribelhorn C, Belda-Ferre P, Ea AC, Bryant M, Young JA, Carrow HC, Sandborn WJ, Dulai PS, Sivagnanam M, Pride D, Knight R, Chu H.mSystems. 2024 Jul 23;9(7):e0051624.Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a comprehensive collection of 694 B. fragilis whole genome sequences, we identify novel features distinguishing these divisions. Our study reveals a distinct geographic distribution with division I strains predominantly found in North America and division II strains in Asia. Additionally, division II strains are more frequently associated with bloodstream infections, suggesting a distinct pathogenic potential. We report differences between the two divisions in gene abundance related to metabolism, virulence, stress response, and colonization strategies. Notably, division II strains harbor more antimicrobial resistance (AMR) genes than division I strains. These findings offer new insights into the functional roles of division I and II strains, indicating specialized niches within the intestine and potential pathogenic roles in extraintestinal sites.
IMPORTANCE: Understanding the distinct functions of microbial species in the gut microbiome is crucial for deciphering their impact on human health. Classifying division II strains as Bacteroides fragilis can lead to erroneous associations, as researchers may mistakenly attribute characteristics observed in division II strains to the more extensively studied division I B. fragilis. Our findings underscore the necessity of recognizing these divisions as separate species with distinct functions. We unveil new findings of differential gene prevalence between division I and II strains in genes associated with intestinal colonization and survival strategies, potentially influencing their role as gut commensals and their pathogenicity in extraintestinal sites. Despite the significant niche overlap and colonization patterns between these groups, our study highlights the complex dynamics that govern strain distribution and behavior, emphasizing the need for a nuanced understanding of these microorganisms. - ArticleGiesecke T, Wolters S, Jahns S, Brande A.PLoS One. 2012;7(12):e51624.In mid to high latitudes glacial and interglacial cycles have repeatedly changed the area available for plant growth. The speed at which plants are able to colonize areas at the onset of an interglacial is hypothesized to limit their distribution ranges even today (migrational lag). If the spread of plants would have been generally slow then plant diversity in previously glaciated areas would be expected to increase over time. We explore this hypothesis using results from six palynological investigations from two previously glaciated regions: central Sweden and north-eastern Germany. Rarefaction, slope of rank order abundance, and taxa accumulation plots were used to evaluate richness and evenness in pollen data in an attempt to separate richness from evenness. These analyses show little change in palynological richness for the northern sites throughout the Holocene. In contrast, the southern sites show an increase in richness and evenness during the early Holocene; this may be explained by the different initial conditions at the onset of the Holocene. A strong rise in palynological richness around 6000 and 1000 years ago at the southern sites can be attributed to the regional initiation of agriculture and major opening of the forest, respectively. For the northern sites there is no evidence for increased taxonomic diversity through time that could be due to delayed immigration of species.
- ArticleSun J, Ke Z, Zhang Y, Wu Q, Chen Y, Tang J.Environ Sci Pollut Res Int. 2023 Apr;30(18):51624-51637.Bays are transition zones connecting freshwater ecosystems and marine ecosystems, and they are strongly influenced by intensive human activities. Pharmaceuticals are of concern in bay aquatic environments because of their potential threat to marine food web. We studied the occurrence, spatial distribution, and ecological risks of 34 pharmaceutical active compounds (PhACs) in Xiangshan Bay, a heavily industrialized and urbanized area in Zhejiang Province, Eastern China. PhACs were ubiquitously detected in the coastal waters of the study area. A total of twenty-nine compounds were detected in at least one sample. Carbamazepine, lincomycin, diltiazem, propranolol, venlafaxine, anhydro erythromycin, and ofloxacin had the highest detection rate (≥ 93%). These compounds were detected with maximum concentrations of 31, 127, 0.52, 1.96, 2.98, 75, and 98 ng/L, respectively. Human pollution activities included marine aquacultural discharge and effluents from the local sewage treatment plants. These activities were the most influential sources in this study area based on principal component analysis. Lincomycin was an indicator of veterinary pollution of coastal aquatic environment, and the concentrations of lincomycin were positively related to the total phosphorus in this area (r = 0.28, p < 0.05). Typical PhACs such as venlafaxine, ofloxacin, norfloxacin, roxithromycin, and clarithromycin were significantly and positively correlated with nitrate and total nitrogen (r > 0.26, p < 0.05) based on Pearson's correlation analysis. Carbamazepine was negatively correlated with salinity (r < - 0.30, p < 0.01). Land use pattern was also correlated with the occurrence and distribution of PhACs in the Xiangshan Bay. Some PhACs, i.e., ofloxacin, ciprofloxacin, carbamazepine, and amitriptyline posed medium to high ecological risks to this coastal environment. The results of this study could be helpful to understand the levels of pharmaceuticals, potential sources, and ecological risks in marine aquacultural environment.
- BookSeema Yasmin.Summary: "Merging documentary poetry from the epicenter of an epidemic with the story of viruses in the evolution of humanity, If God Is A Virus gives voice to the infected and the virus. Based on original reporting from West Africa and the United States, and the poet's experiences as a doctor and journalist, If God Is A Virus charts the course of the largest and deadliest Ebola epidemic in history, telling the stories of Ebola survivors, outbreak responders, journalists and the virus itself. Documentary poems explore which human lives are valued, how editorial decisions are weighed, what role the aid industrial complex plays in crises, and how medical myths and rumor can travel faster than microbes. These poems also give voice to the virus. Eight percent of the human genome is inherited from viruses and the human placenta would not exist without a gene descended from a virus. If God Is A Virus reimagines viruses as givers of life and even authors of a viral-human self-help book"-- Provided by publisher.
Contents:
Disease Is Not the Only Thing That Spreads p. 2
If God Is a Virus p. 3
Smell No Taste, Liberia p. 4
All the News That's Fit to Print p. 5
Liberia, Day Zero p. 6
Youssou N'Dour Cancels His Concert in Conakry p. 8
Dis-ease p. 9
Surrogate Marker p. 10
Lady doctor p. 12
Hippocritic Oath p. 15
If God Is a Virus p. 16
When the White Patient Asks for a White Doctor p. 17
Life of the Party p. 18
My Lover Bathes Me p. 19
Baby Sister Survives Ebola... p. 20
& Dies in Childbirth p. 21
Misfortune Teller p. 22
Ebola News Cento p. 23
A Virus Pens a Self-Help Book p. 25
Filovirus Phylogenetic Tree p. 29
Self-Portrait as Virus p. 30
Anamnesis p. 31
HTBBN p. 35
WHO Said p. 37
WHO Said p. 38
Outbreak Bingo p. 39
We Are Watching p. 40
Misdiagnosis p. 41
Neologisms p. 42
What They Hear When They Listen to Your Heart p. 43
Lead Pipe Dreams: Ghazal for Flint p. 45
WHO Said p. 46
Anti Body p. 47
International Classification of Diseases p. 48
Laylatl Qadr p. 49
The Queen's English p. 50
Grandma Is a Pharmaceutical Chemist p. 51
Forty-One Surah Yaseens p. 52
Dua'a for Crossing Borders p. 54
If God Is a Virus p. 55
If God Is a Computer Virus p. 56
Mango Pickle p. 57
Big Sister Teaches Me How to Ululate p. 58
Hymen Hymn p. 59
Ebola Cento p. 60
Mango Pickle p. 61
Syndemics p. 62
If God Is a Virus p. 63
My God Is a Virus p. 67
Ebola Cento p. 68
NHS Zindabaad! p. 69. - ArticleNakajima Y, Ishibashi J, Yukuhiro F, Asaoka A, Taylor D, Yamakawa M.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):125-30.Defensins are a major group of antimicrobial peptides and are found widely in vertebrates, invertebrates and plants. Invertebrate defensins have been identified from insects, scorpions, mussels and ticks. In this study, chemically synthesized tick defensin was used to further investigate the activity spectrum and mode of action of natural tick defensin. Synthetic tick defensin showed antibacterial activity against many Gram-positive bacteria but not Gram-negative bacteria and low hemolytic activity, characteristic of invertebrate defensins. Furthermore, bactericidal activity against pathogenic Gram-positive bacteria including Bacillus cereus, Enterococcus faecalis and methicillin-resistant Staphylococcus aureus was observed. However, more than 30 min was necessary for tick defensin to completely kill bacteria. The interaction of tick defensin with the bacterial cytoplasmic membrane and its ability to disrupt the membrane potential was analyzed. Tick defensin was able to disrupt the membrane potential over a period of 30-60 min consistent with its relatively slow killing. Transmission electron microscopy of Micrococcus luteus treated with tick defensin showed lysis of the cytoplasmic membrane and leakage of cellular cytoplasmic contents. These findings suggest that the primary mechanism of action of tick defensin is bacterial cytoplasmic membrane lysis. In addition, incomplete cell division with multiple cross-wall formation was occasionally seen in tick defensin-treated bacteria showing pleiotropic secondary effects of tick defensin.
- ArticleVerheesen P, ten Haaft MR, Lindner N, Verrips CT, de Haard JJ.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):21-8.We explored the possibility to apply single-domain antibodies from Camelidae for immunoaffinity purification of the ice structuring protein (ISP) from Lolium perenne, which modifies ice crystal growth and therefore has potential application in medicine, biotechnology, agriculture and (frozen) foods. Using phage display together with an appropriate selection method, a group of candidate fragments was isolated from a llama-derived immune library. Affinity chromatography using a purposely selected antibody coupled to a matrix yielded a completely pure and functional ISP. Due to the extreme refolding capabilities and physical stability of single-domain antibodies, the affinity matrix could be regenerated more than 2000 times without loss of capacity, while the fragment's monomeric nature permitted an efficient elution of antigen. The results of this study show that highly pure proteins can be recovered from biological material in a single-step process.
- ArticleWhite RH.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):46-53.The pathway for the biosynthesis of cysteine and homocysteine in Methanococcus jannaschii has been examined using a gas chromatography-mass spectrometry (GC-MS) stable isotope dilution method to identify and quantitate the intermediates in the pathways. The first step in the pathway, and the one responsible for incorporation of sulfur into both cysteine and methionine, is the reaction between O-phosphohomoserine and a presently unidentified sulfur source present in cell extracts, to produce L-homocysteine. This sulfur source was shown not to be sulfide. The resulting L-homocysteine then reacts with O-phosphoserine to form L-cystathionine, which is cleaved to L-cysteine. The pathway has elements of both the plant and mammalian pathways in that the sulfur is first incorporated into homocysteine using O-phosphohomoserine as the acceptor and the resulting homocysteine, via transsulfuration, supplies the sulfur for cysteine formation. The pathway leading to these two amino acids represents an example of metabolic thrift where the preexisting cellular metabolites O-phosphohomoserine and O-phosphoserine are used as the ultimate source of the carbon framework for the biosynthesis of these amino acids. These findings explain the absence of identifiable genes in the genome of this organism for the biosynthesis of cysteine and homocysteine.
- ArticleKempson IM, Skinner WM, Kirkbride PK.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):1-5.Calcium distributions on internal and external surfaces of longitudinally sectioned hairs were analysed with Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS). Externally, calcium deposits were observed at the cuticle scale edges. Internal sections showed that the bulk of calcium exists within or just inside the cuticle layer. The medulla may or may not be enriched and other localised concentrations exist in one of two forms; either associated with granular structures or the hair proteins. Calcium appears to show an affinity for proteins with low sulfur content.
- ArticleBiró A, Hérincs Z, Fellinger E, Szilágyi L, Barad Z, Gergely J, Gráf L, Sármay G.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):60-9.Activated B cells may cleave their surface receptors due to the proteolytic activity on the cell membrane or in its vicinity. We attempted to isolate and characterize the protease(s) responsible for this cleavage. Zymograms prepared from the supernatant and the plasma membrane fraction of activated human B cells and BL41/95 cell line exhibited a 85-90 kDa doublet band with protease activity, while that of resting B cells did not. Soybean trypsin inhibitor (STI), Nalpha-p-tosyl-L-lysine chloromethyl ketone (TLCK) and EDTA treatment abolished the activity of this protease. The excess of Zn(2+) ions in EDTA did not restore the enzymatic activity, while it was completely recovered in the presence of Ca(2+). We affinity-purified a 85-90 kDa protease from the supernatant of BL41/95 cells using STI coupled to Sepharose 4B beads, and measured its kinetic parameters. For the arginyl substrate K(M) was 358+/-59 microM and for the lysyl substrate 582+/-103 microM. TLCK and benzamidine inhibited the protease at micromolar, while STI at nanomolar concentrations. Both the inhibition profile and the substrate specificity suggest that it is a trypsin-like serine protease. We assume that the 85-90 kDa serine protease expressed on and secreted by activated B cells and BL41/95 cell line is responsible for the cleavage of various membrane proteins, including Fcgamma receptors; thus it may play a crucial role in regulating B cell's function.
- ArticleSakamoto T, Ihara H, Kozaki S, Kawasaki H.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):70-5.Previously, three arabinan-degrading enzymes were isolated from Penicillium chrysogenum 31B. Here we describe another arabinan-degrading enzyme, termed Abnc, from the culture filtrate of the same organism. Analysis of the reaction products of debranched arabinan by high-performance anion-exchange chromatography (HPAEC) revealed that Abnc cleaved the substrate in an endo manner and that the final major product was arabinotriose. The molecular mass of Abnc was estimated to be 35 kDa by SDS-PAGE. Enzyme activity of Abnc was highest at pH 6.0 to 7.0. The enzyme was stable up to 30 degrees C and showed optimum activity at 30 to 40 degrees C. Compared with a mesophilic counterpart from Aspergillus niger, Abnc exhibited a lower thermal stability and optimum enzyme activity at lower temperatures. Production of Abnc in P. chrysogenum was found to be strongly induced by arabinose-containing polymers and required a longer culture time than did other arabinanase isozymes in this strain.
- ArticleYoshioka Y, Suzuki R, Okamoto T, Okada N, Mukai Y, Shibata H, Tsutsumi Y, Dohi N, Okada N, Nakagawa S, Mayumi T.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):54-9.We previously reported the development of a "cytomedicine" that consists of cells trapped in alginate-poly-L-lysine-alginate (APA) microcapsules and agarose microbeads. The functional cells that are entrapped in semipermeable polymer are completely isolated from cellular immune system. However, the ability of cytomedicine to isolate cells from the humoral immune system, which plays an essential role in xenograft rejection, is low. Therefore, the goal of the present study was to develop a novel cytomedicine that could protect the entrapped cells from injury of the complement system. We investigated the applicability of the complement regulatory protein (CRP), Crry, to cytomedicine. Crry-transfected cells entrapped within agarose microbeads resisted injury by complement to a degree, while entrapment of Crry transfected cells within agarose microbeads containing polyvinyl sulfate (PVS), a novel cytomedical device with anti-complement activity, clearly protected against complement attack. These data indicate that the combination of a CRP and a cytomedical device with anti-complement activity is a superior device for cytomedical therapy.
- ArticleSachs NA, Vaillancourt RR.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):98-108.Cyclin-dependent kinase (CDK)11(p110), formerly known as PITSLRE, is a serine/threonine kinase whose catalytic activity has been associated with transcription and RNA processing. To further evaluate the regulation of CDK11(p110) catalytic activity, interacting proteins were identified by liquid chromatography and tandem mass spectrometry (LC-MS/MS). Following the immunoprecipitation of CDK11(p110) from COS-7 cells, the serine/threonine kinase CK2 was identified by LC-MS/MS. These results were extended through the observation that CDK11(p110) serves as a substrate for CK2 and the identification of a phosphorylation site on CDK11(p110) at Ser227 by LC-MS/MS. To obtain CDK11(p110) devoid of CK2, CDK11(p110) was expressed in High Five insect cells and secreted into the media due to the presence of a honeybee melittin signal sequence encoded at the amino-terminus of CDK11(p110). Recombinant CDK11(p110) was purified from the media and phosphorylation of histone H1 subsequently demonstrated. After demonstrating retention of CDK11(p110) kinase activity, it was evaluated for activity on the carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAP II), but only CK2 was found to phosphorylate the CTD.
- ArticleOhl CD, Wolfrum B.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):131-8.The interaction of lithotripter-generated shock waves with adherent cells is investigated using high-speed optical techniques. We show that shock waves permeabilize adherent cells in vitro through the action of cavitation bubbles. The bubbles are formed in the trailing tensile pulse of a lithotripter-generated shock wave where the pressure drops below the vapor pressure. Upon collapse of cavitation bubbles, a strong flow field is generated which accounts for two effects: first, detachment of cells from the substrate; and second, the temporary opening of cell membranes followed by molecular uptake, a process called sonoporation. Comparison of observed cell detachment with results from a theoretical model considering peeling cell detachment by a wall jet-induced shear stress shows reasonable agreement.
- ArticleAntunes F, Marinho HS, Barreto MC, Pavão ML, Pinto RE.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):11-20.In this work, a method for the diagnosis of kinetic inhibition, based on the dependence of the degree of inhibition (epsilon(i)) on the inhibitor concentration [I] and on the substrate concentration [S], is presented. Because the degree of inhibition is a ratio between rates, kinetic data are normalized by the introduction of an internal control-the rate of the uninhibited reaction. Therefore, the error associated with the kinetic measurements decreases and less experimental measurements are necessary to achieve the diagnosis. The process described, which uses graphical and/or non-linear fitting procedures, allows distinguishing between 20 different kinds of inhibition, including not only linear and hyperbolic, but also parabolic and rational 2,2 inhibitions. Rational 2,2 indicates a new type of inhibition corresponding to an incomplete parabolic inhibition, i.e. mechanistically it corresponds to an inhibitor that binds to two inhibition sites producing enzymatic complexes that are still active. In spite of its comprehensiveness, the diagnosis process is greatly facilitated by the division of the diagnosis of the inhibition in a step-by-step procedure, where only two rival models are evaluated in each step. In the non-linear fittings, the choice between rival models uses a test based on information statistics theory, the Akaike information criterion test, in order to penalize complex models that tend to be favoured in fittings. Finally, equations that allow the determination of inhibition kinetic constants were also deduced. The formalism presented was tested by examining inhibition of acid phosphatase by phosphate (a linear competitive inhibitor).
- ArticleBrooks AS, Hammermueller J, DeLay JP, Hayes MA.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):36-45.Ficolins are collagenous lectins that bind N-acetylglucosamine (GlcNAc) as well as some bacterial surfaces, and may have opsonic and complement-activating functions. Ficolin alpha in porcine plasma binds Actinobacillus pleuropneumoniae serotype 5 (APP) in a GlcNAc-dependent manner. In the present study, we discovered that porcine neutrophils, but not platelets or mononuclear cells, contained a different ficolin that migrated as a 39-kDa band on SDS-PAGE and resembled a minor component of plasma ficolins that binds APP. However, neutrophil ficolins (pI range 6.4-7.4) were readily distinguished from plasma ficolin alpha (pI 5.2-5.8) by 2D PAGE. Neutrophil ficolin was consistent with ficolin beta by pI and peptide mass fingerprinting with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Porcine neutrophils expressed ficolin beta, but not ficolin alpha, as determined by RT-PCR. Ficolin beta was present in the membrane and cytoplasmic fractions of nonactivated neutrophils, but the majority of ficolin beta was secreted upon activation with PMA. Ficolin alpha readily bound to intact APP, but ficolin beta did not under the same conditions. These studies demonstrate that neutrophils express ficolin beta and secrete it when activated; however, ficolin beta may have different binding functions than ficolin alpha.
- ArticleAmi D, Bonecchi L, Calì S, Orsini G, Tonon G, Doglia SM.Biochim Biophys Acta. 2003 Dec 05;1624(1-3):6-10.Two recombinant Escherichia coli strains expressing different levels of an interferon fusion protein as inclusion bodies have been studied by Fourier transform infrared (FT-IR) microspectroscopy. A marker band at 1628 cm(-1) allowed monitoring of the protein expression by direct analysis of cell pellets in a rapid, non-invasive and quantitative way. The results demonstrate that FT-IR microspectroscopy is a technique of potential biotechnological interest for studying inclusion body formation.