Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells.

The crowded bacterial cytoplasm is comprised of biomolecules that span several orders of magnitude in size and electrical charge. This complexity has been proposed as the source of the rich spatial organization and apparent anomalous diffusion of intracellular components, although this has not been tested directly. Here, we use biplane microscopy to track the 3D motion of self-assembled bacterial Genetically Encoded Multimeric nanoparticles (bGEMs) with tunable size (20 to 50 nm) and charge (-2160 to +1800 e) in live Escherichia coli cells. To probe intermolecular details at spatial and temporal resolutions beyond experimental limits, we also developed a colloidal whole-cell model that explicitly represents the size and charge of cytoplasmic macromolecules and the porous structure of the bacterial nucleoid. Combining these techniques, we show that bGEMs spatially segregate by size, with small 20-nm particles enriched inside the nucleoid, and larger and/or positively charged particles excluded from this region. Localization is driven by entropic and electrostatic forces arising from cytoplasmic polydispersity, nucleoid structure, geometrical confinement, and interactions with other biomolecules including ribosomes and DNA. We observe that at the timescales of traditional single molecule tracking experiments, motion appears sub-diffusive for all particle sizes and charges. However, using computer simulations with higher temporal resolution, we find that the apparent anomalous exponents are governed by the region of the cell in which bGEMs are located. Molecular motion does not display anomalous diffusion on short time scales and the apparent sub-diffusion arises from geometrical confinement within the nucleoid and by the cell boundary.

Colloidal Physics Modeling Reveals How Per-Ribosome Productivity Increases with Growth Rate in Escherichia coli.

Faster-growing cells must synthesize proteins more quickly. Increased ribosome abundance only partly accounts for increases in total protein synthesis rates. The productivity of individual ribosomes must increase too, almost doubling by an unknown mechanism. Prior models point to diffusive transport as a limiting factor but raise a paradox: faster-growing cells are more crowded, yet crowding slows diffusion. We suspected that physical crowding, transport, and stoichiometry, considered together, might reveal a more nuanced explanation. To investigate, we built a first-principles physics-based model of Escherichia coli cytoplasm in which Brownian motion and diffusion arise directly from physical interactions between individual molecules of finite size, density, and physiological abundance. Using our microscopically detailed model, we predicted that physical transport of individual ternary complexes accounts for ~80% of translation elongation latency. We also found that volumetric crowding increases during faster growth even as cytoplasmic mass density remains relatively constant. Despite slowed diffusion, we predicted that improved proximity between ternary complexes and ribosomes wins out, illustrating a simple physics-based mechanism for how individual elongating ribosomes become more productive. We speculate that crowding imposes a physical limit on growth rate and undergirds cellular behavior more broadly. Unfitted colloidal-scale modeling offers systems biology a complementary "physics engine" for exploring how cellular-scale behaviors arise from physical transport and reactions among individual molecules. IMPORTANCE Ribosomes are the factories in cells that synthesize proteins. When cells grow faster, there are not enough ribosomes to keep up with the demand for faster protein synthesis without individual ribosomes becoming more productive. Yet, faster-growing cells are more crowded, seemingly making it harder for each ribosome to do its work. Our computational model of the physics of translation elongation reveals the underlying mechanism for how individual ribosomes become more productive: proximity and stoichiometry of translation molecules overcome crowding. Our model also suggests a universal physical limitation of cell growth rates.

An improved platform for cultured neuronal network electrophysiology: multichannel optogenetics integrated with MEAs.

Cultured neuronal networks (CNNs) are powerful tools for studying how neuronal representation and adaptation emerge in networks of controlled populations of neurons. To ensure the interaction of a CNN and an artificial setting, reliable operation in both open and closed loops should be provided. In this study, we integrated optogenetic stimulation with microelectrode array (MEA) recordings using a digital micromirror device and developed an improved research tool with a 64-channel interface for neuronal network control and data acquisition. We determined the ideal stimulation parameters including light intensity, frequency, and duty cycle for our configuration. This resulted in robust and reproducible neuronal responses. We also demonstrated both open and closed loop configurations in the new platform involving multiple bidirectional channels. Unlike previous approaches that combined optogenetic stimulation and MEA recordings, we did not use binary grid patterns, but assigned an adjustable-size, non-binary optical spot to each electrode. This approach allowed simultaneous use of multiple input-output channels and facilitated adaptation of the stimulation parameters. Hence, we advanced a 64-channel interface in that each channel can be controlled individually in both directions simultaneously without any interference or interrupts. The presented setup meets the requirements of research in neuronal plasticity, network encoding and representation, closed-loop control of firing rate and synchronization. Researchers who develop closed-loop control techniques and adaptive stimulation strategies for network activity will benefit much from this novel setup.

22.5 MB DELETION OF 13q31.1-q34 ASSOCIATED WITH HPE, DWM, AND HSCR: A CASE REPORT AND REDEFINING THE SMALLEST DELETED REGIONS.

Partial deletion of the long arm of the chromosome 13, 13q deletion syndrome is a rare chromosomal disorder characterized by severe growth and mental retardation, microcephaly, facial dysmorphism, brain malformations (holoprosencephaly, Dandy-Walker malformation), distal limb defects, eye anomalies, genitourinary and gastrointestinal tract malformations (Hirschsprung's disease). Approximately 1.2 Mb region in 13q32 was suggested as minimal critical region which is responsible for severe mental and growth retardation and brain anomalies. Here we described a male patient with de novo interstitial deletion of 13q31.1-q34 associated with short stature, microcephaly, facial dysmorphism, clinodactyly, cryptorchidism, micropenis, epilepsy, HPE, DWM, and HSCR. According to the literature review, present case indicated that smallest deleted region associated with DWM and HPE might be located at the 13q32.3, limb defects 13q34, anogenital malformations 13q33.3-34, and HSCR 13q31.1-32.1.

Co-administration of cisplatin and curcumin does not alter mood-associated behaviors.

OBJECTIVES: Cisplatin (cis-diamminedichloroplatinum (II)) is a widely-used platinum-based chemotherapeutic agent which has dose-limiting side-effects. Also, the drug resistance is another instance that decreases treatment success in cisplatin chemotherapy. The growing body of evidence suggests that curcumin, a polyphenolic compound extracted from the spice turmeric, may exert synergistic effects and sensitize malign cells to cisplatin, while alleviating cytotoxicity-related side-effects. The present study was aimed to investigate mood-associated interactions between cisplatin and curcumin. MATERIALS AND METHODS: Thirty-four adult male Wistar albino rats were randomly assigned to four groups as control, curcumin (300 mg/kg/day, p.o. for 5 weeks), cisplatin (5 mg/kg/week, i.p. for 5 weeks), and curcumin plus cisplatin (same doses as above). The open field, elevated plus maze, and forced swim tests were engaged to evaluate mood-associated behaviors. RESULTS: We demonstrated that depression- and anxiety-like behaviors were not altered by the administration of curcumin along with the chronic cisplatin treatment. CONCLUSION: According to the results of the present study, we concluded that curcumin might be regarded as a safe adjuvant in cisplatin chemotherapy in terms of the mood-associated behaviors (Fig. 4, Ref. 41).

A familial case of Coffin-Lowry syndrome caused by RPS6KA3 C.898C>T mutation associated with multiple abnormal brain imaging findings.

Coffin-Lowry syndrome (CLS) is a rare X linked mental retardation syndrome characterised by severe psychomotor and growth retardation, distinct facial phenotype, and progressive skeletal malformations. It is caused by mutations in the RPS6KA3 gene located at Xp22.2. In this report we describe a family with CLS consists of three affected males, and two affected females, arising from c.898C>T mutation in RPS6KA3 gene. A 6 year-old, and a 3 year-old boy both had distinct clinical features of Coffin-Lowry syndrome; severe mental and motor retardation, microcephaly, prominent forehead, hypertelorism, large mouth, large ears, large soft hands, puffy tapered fingers, and pectus carinatum. In addition, they had multiple abnormal brain MRI findings. Other siblings presented with a mild and variable phenotype.

Late coronary stent dislodgement following coronary artery stenting.

Recently, coronary artery stenting has been successful when used as an intervention for percutaneous coronary artery disease. However, the procedure may frequently produce complications. Although rare, stent dislodgement is one such complication, which may result in serious problems including coronary artery dissection, myocardial infarction, peripheral embolisation and death. Stent dislodgement is known to be an early complication of the coronary artery stenting procedure. In this case report, we present a 53-year-old male with late coronary stent dislodgement. To the best of our knowledge, no such case has been addressed in the literature to date.

De novo interstitial deletion of 9q32-34.1 with mental retardation, developmental delay, epilepsy, and cortical dysplasia: a case report.

In this report we describe a 10 year-old female patient with interstitial deletion of 9q32-q34.1 associated with mental retardation, developmental delay, short stature, mild facial dysmorphism, epilepsy, abnormal EEG and brain MRI findings consistent with focal cortical dysplasia. Interstitial deletion of 9q associated with q32-q34 is found extremely rare. Common features of seven previously reported cases are mental retardation, developmental delay, short stature, a distinct cranial and facial phenotype (brachycephaly, low midface, low and prominent forehead, and low set malformed ears). Combination of epilepsy, abnormal EEG and brain MRI findings are not reported before.

Partial monosomy 8q and partial trisomy 9q due to the maternal translocation t(8;9(q24.3;q34.1): a case report.

Partial trisomy 9q34-qter and partial monosomy 8q24.3-qter are very rare chromosomal abnormalities. Characteristic features of partial trisomy 9q34-qter are hypotonia, developmental delay, mild intellectual disability, dolichocephaly, distinct facial phenotype, long and thin fingers, and cardiac anomalies. Unlike the partial trisomy 9q34-qter, partial monosomy 8q24.3-qter has no distinct phenotype. Here we report a four years old female patient with partial trisomy 9q34-qter and partial monosomy 8q24.3-qter due to the maternal translocation t(8;9)(q24.3;q34. I). She has developmental delay, brachycephaly, facial dysmorphism, hand and foot anomalies, bilateral hearing loss, cardiac defect and abnormal brain MRI findings. To the best of our knowledge, this is the first report of the combination of partial trisomy 9q and partial monosomy 8q.

Genetics analysis with down syndrome and histopathological examination of buccal epithelial cells / Análisis genético y examen histopatológico de las células epiteliales bucales en pacientes con síndrome de down

Down syndrome is primarily caused by trisomy of chromosome 21. We reviewed cytogenetic studies performed on 1048 patients who were referred to the Cytogenetics Unit at Dicle University Hospital, Diyarbakir, Southeast Turkey, between 2000 and 2009. The cases were grouped according to the reason of referral for cytogenetic analysis. The highest frequencies of abnormal karyotypes were found among cases that were referred due to suspicion of Down syndrome (84.8 percent). For histologic examination to persons with Down syndrome and normal, buccal mucosa smear was prepared by rubbing. Down syndrome are disabled and control groups were compared statistically buccal epithelial cells and nuclei (p<0.05). Periphery of the nucleus in some patients with Down's syndrome, while the bud structures in the form of micronuclei was observed in the karyolytic cells.

El síndrome de Down es causado principalmente por la trisomía del cromosoma 21. Se revisaron los estudios citogenéticos realizados en 1.048 pacientes que fueron remitidos a la Unidad de Citogenética del Dicle University Hospital, Diyarbakir, sudeste de Turquía, entre los años 2000 y 2009. Los casos se agruparon de acuerdo a la razón de referencia para el análisis citogenético. Las frecuencias más altas de cariotipos anormales se encontraron ent los casos que fueron remitidos por sospecha de síndrome de Down (84,8 por ciento). Para el estudio histológico de las personas con y sin síndrome de Down, se realizó el frotis de mucosa oral por hisopado. Los grupos con síndrome de Down y de control (sin síndrome) se compararon estadísticamente en relación a las células epiteliales orales y los núcleos (p <0,05). Se observaron núcleos periféricos en algunos pacientes con síndrome de Down, mientras que estructuras de tipo brotes en la forma de micronúcleos se observaron en las células cariolíticas.

Chromosome heteromorphisms are more frequent in couples with recurrent abortions.

Chromosomal heteromorphism is considered a variant of a normal karyotype, but it is more frequent in couples with repeated miscarriages. We investigated chromosomal heteromorphism in couples with repeated miscarriages in comparison with a control group. A total of 455 couples who applied to our genetic diagnosis laboratory in Diyarbakir, Turkey, were evaluated for chromosome heteromorphisms; 221 of these couples (the study group) had recurrent abortions and 234 of them (the control group) had no history of abortions and had at least one living child. The patient group of couples with recurrent abortions were found to have a significantly higher rate of chromosome heteromorphism (8.4%) in comparison with the control group (4.9%). When the patients were evaluated according to gender, males had a significantly higher rate of chromosome heteromorphism (11.3%) than females (5.4%). We conclude that since couples with recurrent abortion and males have higher rate of chromosome heteromorphism, cases of heteromorphism should not be disregarded in the etiological investigation of recurrent abortions. Further research should be done to investigate the phenotypic effects of chromosome heteromorphism.

A case of onycotricodysplasia with intellectual disability, without neutropenia.

Onychotrichodysplasia, a rare autosomal recessive disorder, presents with hypoplastic fingernails, trichorrhexis, chronic neutropenia, and psychomotor retardation. Here, we describe a rare presentation of a child with onycotrichodysplasia associated with intellectual disability, but without neutropenia. He had sparse, short, dry, curly hair, dysplastic nails and intellectual disability. In contrast to cases described earlier, our patient had normal neutrophil count.

Comparison of broiler meat quality when fed diets supplemented with neutralized sunflower soapstock or soybean oil.

The objective of the current study was to evaluate the effect of dietary fat type and level on broiler meat quality. A 2 × 3 factorial arrangement with 2 types of fat including neutralized sunflower soapstock (NSS) and soybean oil (SO) at 3 levels of fat inclusion (2, 4, and 6%) was used with 5 replicates per treatment using 750 one-day-old broiler chicks in a completely randomized design. At the end of the study (d 36), 10 broilers from each replication were processed at a commercial slaughtering facility. Six carcasses from each replicate were used for meat quality evaluation. With the exception of 3 responses [breast meat lightness (L*) at 1 and 2 d, and redness (a*) at 5 d], there were no interactions between fat source and level. Breast meat pH at 15 min was not significantly affected by the dietary treatments. However, breast meat pH at 24 h postmortem was decreased (P < 0.01) in broilers fed the NSS. Breast meat cooking loss, shear force, and color did not differ between fat sources. Breast meat cooking loss decreased (P < 0.05) when the dietary levels of fat increased. Thigh meat TBA reactive substances were not different due to dietary fat source and level. Breast meat and skin L* value significantly decreased when the dietary levels of fat increased. Breast meat a* value was highest for the 6% fat fed birds on d 2 (P < 0.05) and d 5 (P < 0.01). Higher dietary fat levels decreased the b* values of breast meat except d 5. Breast skin yellowness (b*) value was higher (P < 0.01) for the SO-fed birds compared with NSS-fed birds. Thigh meat of the birds fed the NSS was lighter (P < 0.05) than that of the birds fed SO diets except d 5. Overall, data suggest that NSS can be used as an alternative fat source to SO with little effect on meat quality.

A case of complete tetraploidy in amniocentesis with normal karyotype in subsequent cordocentesis.

We report a case of complete tetraploidy in amniotic fluid culture obtained at 17 wk of pregnancy. Amniocentesis was performed in this pregnancy because of a high-risk maternal serum screening result and abnormal ultrasound findings. Amniotic fluid was cultured in two flasks. Growth was very slow in one culture with no growth in the other. Harvest was possible after 3 wk, which revealed tetraploidy in all studied plates. Subsequent cordocentesis was performed to confirm the diagnoses of amniocentesis. Chromosomal analysis of the cordocentesis revealed a normal karyotype with 46,XY. A healthy male infant was born at term. This case illustrates that abnormal karyotypes in poor growth cultures could be misleading and should be confirmed by another technique, such as cordocentesis.

Different chromosome Y abnormalities in a case with short stature.

We report a case with different chromosome Y abnormalities. Case was an 11-year-old boy, who was diagnosed with short stature, referred to laboratory of human medical genetics laboratory for genetic evaluation. Chromosomal analysis of the case was carried out on peripheral blood lymphocyte culture. Classic cytogenetic analysis (G and C banding) was confirmed by using fluorescence in situ hybridization analysis (FISH) technique. Cytogenetic and FISH analysis showed a mosaic 46,X,i(Yq)/45,X/47,X,i(Yq)x2/47,XYY karyotype. Case, which was found interesting due to its rarity, is discussed with its clinical features and cytogenetic results, in the light of relevant source information. This case underlines the importance of karyotyping patients with unexplained short stature. This clinical report also will be helpful in defining the phenotypic range associated with these karyotypes.

The evaluation of genotoxic potential of ornidazole, nitroimidazole, in lymphocyte culture of patients with amebiasis.

The genotoxicity study of ornidazole (ONZ) was carried out on human lymphocyte chromosomes, using sister chromatid exchange (SCE) and micronucleus (MN). Thirty-two patients with Entemoeba histolitica infection who received 1000 mg/day for 10 days were included in this study. SCE and MN were measured before and after therapy. A statistically significant increase was observed in the SCE (P < 0.001) and MN frequencies (P < 0.001) after ornidazole therapy. It was concluded that ONZ has a potential geno- and cytotoxic effect in human peripheral lymphocyte cultures. For this reason, further, detailed studies are needed to elucidate the ONZ mechanism of genotoxicity and its carcinogenic potential.

Evaluation of clinical and cytogenetic findings on 1,068 second-trimester amniocenteses in Southeast Turkey.

OBJECTIVE: To investigate the indications of amniocentesis for the detection of chromosomal abnormalities among a sample of patients in Southeast Turkey. MATERIAL AND METHODS: Between 2004 and 2007, 1,068 second-trimester amniocentesis tests were performed in the Medical Biology and Genetics Department Laboratory at Dicle University. Amniotic fluids were cultured by using long-term tissue culture for prenatal diagnosis with cytogenetic analysis. The clinical and cytogenetic findings on 1,068 second-trimester amniocenteses were analyzed. The indications, the proportions of karyotypes according to indications and complications were summarized. RESULTS: Among the 1,068 amniocentesis cases, the maternal age between 35 and 39 years was the most common age group (34.5%). Of the clinical indications abnormal maternal serum screening results were the most common indication for amniocentesis (37.6%). Of 52 cases (4.9%) with detected chromosomal aberrations, 39 were numeric (27 trisomies, 10 sex chromosome aberrations and two triploidies) and 13 were structural (2 reciprocal translocations, 2 Robertsonian translocations and 6 inversions). The highest detection rate of chromosome aberrations was in cases undergoing amniocentesis for abnormal maternal serum screening combined with abnormal ultrasound (US) findings (8.0%). CONCLUSION: This study suggests that complementary measures, such as routine antenatal US and maternal serum screening, should be added to increase the efficiency of genetic amniocentesis. Therefore, the study could be used for the establishment of a database for genetic counseling.

Cytogenetic analysis of 4216 patients referred for suspected chromosomal abnormalities in Southeast Turkey.

We reviewed cytogenetic studies performed on 4216 patients who were referred to the Cytogenetics Unit at Dicle University Hospital, Diyarbair, Southeast Turkey, between 2000 and 2009. The cases were grouped according to the reason of referral for cytogenetic analysis. The frequencies of the different types of numerical and structural abnormalities were determined, and the relative frequency of cases with abnormal karyotypes was calculated in each group. The most common reason for requesting cytogenetic testing was referral for Down syndrome and for repeated abortions. The highest frequencies of abnormal karyotypes were found among cases that were referred due to suspicion of Down syndrome (84.8%). Among the chromosomal abnormalities, sexual chromosomal abnormalities were found in 239 cases (17.6%), and Klinefelter syndrome was the most frequent sex chromosomal abnormality. Autosomal abnormalities were found in 1119 cases (82.4%), and Down syndrome was the most frequent autosomal chromosomal abnormality. In conclusion, the high rate of chromosomal abnormalities (32.2%) found in this population demonstrates the importance of cytogenetic evaluation in patients who show clinical abnormalities. This is the first report on cytogenetic testing in the southeast region of Turkey. This type of study provides a basis for determining the risks of recurrence and for deciding on clinical treatment and genetic counseling.