bluuebunny/crossref_metadata_2025 huggingface dataset:
Interactions between the 5′ UTR mRNA of the spe2 gene and spermidine regulate translation in S. pombe
Authors: Sun Wenxia , Zhang Xuhui , Chen Dongrong , Murchie Alastair I.H.
Published: December 2019

The 5′ untranslated regions (5′ UTR) of mRNAs play an important role in the eukaryotic translation initiation process. Additional levels of translational regulation may be mediated through interactions between structured mRNAs that can adopt interchangeable secondary or tertiary structures and the regulatory protein/RNA factors or components of the translational apparatus. Here we report a regulatory function of the 5′ UTR mRNA of the spe2 gene (SAM decarboxylase) in polyamine metabolism of the fission yeast Schizosaccharomyces pombe. Reporter assays, biochemical experiments, and mutational analysis demonstrate that this 5′ UTR mRNA of spe2 can bind to spermidine to regulate translation. A tertiary structure transition in the 5′ UTR RNA upon spermidine binding is essential for translation regulation. This study provides biochemical evidence for spermidine binding to regulate translation of the spe2 gene through interactions with the 5′ UTR mRNA. The identification of such a regulatory RNA that is directly associated with an essential eukaryotic metabolic process suggests that other ligand-binding RNAs may also contribute to eukaryotic gene regulation.
Screening, diagnosis and genetic study of breast cancer patients in Pakistan
Authors: Majeed Ayesha Isani , Ullah Asmat , Jadoon Muniba , Ahmad Wasim , Riazuddin Sheikh
Published: December 2019

Objective: To determine the role of variants in BRCA1 gene in breast cancer development, women of Pakistani origin, diagnosed with breast cancer, were screened for variants in the BRCA1.

Methods: The present study involved screening of 5000 women for breast cancer. 302 women were diagnosed with breast cancer. Using Sanger sequencing, DNA extracted from peripheral blood of 100 patients was screened for disease causing variants in the BRCA1.

Results: Analysis of sequenced data revealed two frame shift (Gly312Trpfs*8, Ala322Glyfs*4), six missense (p.Glu362Lys, p.Lys651Arg, p.Asp693Asn, p.Pro871Leu, p.Glu1134Lys, p.Lys1183Arg), four synonymous (p.Thr327Thr, p.Ser694Ser, p.His771His, p.Gln1135Gln), and two intronic variants (g.75407T>C, g.75401_75401delT) in the patients.

Conclusion: The present investigation showed that variations in BRCA1 made substantial contribution in causing hereditary/early-onset breast cancer in Pakistani women.

doi: https://doi.org/10.12669/pjms.36.1.1059

How to cite this:Majeed AI, Ullah A, Jadoon M, Ahmad W, Riazuddin S. Screening, diagnosis and genetic study of breast cancer patients in Pakistan. Pak J Med Sci. 2020;36(1):---------. doi: https://doi.org/10.12669/pjms.36.1.1059

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Evaluation of endoscopic variceal band ligation sessions in obliteration of esophageal varices
Authors: Alvi Haris , Zuberi Bader Faiyaz , Rasheed Tazeen , Ibrahim Muhammad Asad
Published: December 2019

Objective: To determine number of sessions of Endoscopic variceal band ligation required to obliterate the esophageal varices.

Methods: This study was conducted at Civil Hospital Karachi between June 2018 to April 2019. All patients undergoing endoscopic Variceal Band Ligation (EVBL) were inducted. Number of sessions of band ligation required to obliterate the varices were recorded. Number of EVBL sessions were correlated with Child-Pugh’s Score and etiology of CLD by χ2 test, while it was compared with duration of Chronic Liver Disease (CLD) by One-way ANOVA test.

Results: One hundred ninety-two patients fulfilling selection criteria were admitted after informed consent. These included 101 (52.6%) males and 91 (47.4%) females. Most common cause of cirrhosis was HCV (66.7%) in our patients. Most of the patients were in Child Class-B (71.9%). Majority of patients (52.6%) underwent 3 sessions of EVBL while 68 (35.4%) underwent 4 sessions of EVBL. Duration of CLD was analyzed with number of sessions of EVBL by One-Way ANOVA test and it showed significant more sessions of EVBL were done with longer duration of CLD (p <0.001).

Conclusion: Most patients underwent 3-4 sessions of EVBL for obliteration of varices. Number of EVBL sessions increased significantly with duration of disease.

doi: https://doi.org/10.12669/pjms.36.1.1144

How to cite this:Alvi H, Zuberi BF, Rasheed T, Ibrahim MA. Evaluation of endoscopic variceal band ligation sessions in obliteration of esophageal varices. Pak J Med Sci. 2020;36(1):---------. doi: https://doi.org/10.12669/pjms.36.1.1144

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Particularities of complex therapeutically-rehabilitative management, stepwise, in a patient with post-CCT psycho-cognitive impairment in a large polytraumatic context - case report
Authors: POPESCU Laura Georgiana , NIRLU Luminița , ALBEȘTEANU Ana Carmen , SAGLAM Ali Osman , STAVRICĂ Alexandru , ONOSE Gelu
Published: December 2019

Abstract
The subject matter of the present scientific paper is the report of a sustained, sequential, stage-adjusted and persistent therapeutic rehabilitation team-run program over a relatively short period of time in the case of a polytraumatized patient with severe TBI (GCS=4), multiple pelvic fractures, right clavicle fracture, incomplete fracture of the left transverse apophysis L5 - unoperated, perivesical hematoma, thoraco-abdominal contusion, neurogenic bladder and antero-retrograde amnesia related to trauma that led to a favorable progression despite the contraindication of sitting positioning and the mental state of the patient during hospitalization.

Key words: neuromuscular rehabilitation, cranio-cerebral trauma, pelvic fracture, polytraumatism, antero-retrograde amnesia related to trauma,
Ionophoresis and LASER applications in facial nerve palsy
Authors: DAIA Cristina Octaviana , CROITORU Ștefana , CAZACU Ioana , SCUTUROIU Ruxandra , DAIA Octaviana , AXENTE Mariana , GHERGHICEANU Alina , POP Eduard Stefan , ONOSE Gelu
Published: December 2019

Background and aim of the study. The aim of this article is to present the functional gain of the specific rehabilitation program in patients with facial nerve paralysis, irrespective of etiology, following a complex physiotherapeutic treatment, consisting of the combined application of ionophoresis and LASER.
Material and Method. We performed a retrospective analysis of 26 patients having their consent and The Theaching Emergency Hospital “Bagdasar-Arseni” (TEHBA) ethics Committee’s approval, N.O. 683/21.02.2019. The patients were admitted to the Neuro-Muscular Rehabilitation Clinic Division of TEHBA between April 2011 and March 2019. The patients were over the age of 18, diagnosed with facial nerve palsy and received physiotherapy consisting of the combined application of: ionophoresis with 1% potassium iodide, applied to positive electrode, preauricular, and the negative electrode, retroauricular, for 20 minutes and LASER, to the temporomandibular joint on the affected part, 4 points : radiant exposure per dose 3 J/cm2, frequency 5 Hz, probe area 1 cm2, power 62 mW, for 10 sessions and two sets of the same formula at the temporomandibular joint on the opposite side.
Results. From the etiological point of view, the study included an equal number of patients with peripheric facial palsy (PFP) and with central facial palsy (CFP), respectively 13 in each group. Overall, at least 1 patient in 2 had a positive response to physiotherapy. In the patients with PFP, 77% of patients responded to the treatment and 46% had complete remission. In the patients with CFP, only 30% responded to treatment and only one had complete remission. Approximately half of the patients did not have any adverse reactions (46%), while the rest showed temporary erythema (46%), or local tingling sensation over a variable period of time (8%).
Conclusion. Applying the combination of ionophoresis and LASER as physiotherapic treatment is particularly effective in peripheric facial nerve paresis. The method is safe and well tolerated, therefore we propose its use in this type of pathology.
Key words: Laser therapy, facial nerve paralysis, ionophoresis,
Reporting of academic degrees in high-impact medical journals
Authors: Stankovic Nikola , Nolan Jerry P. , Andersen Lars W.
Published: December 2019

Academic degrees following author names are often included in medical research papers. However, it remains unclear how many journals choose to include academic degrees and whether this is more common in certain types of journals. We examined the 100 highest impact medical journals and found that only 24 medical journals reported academic degrees. Moreover, this was substantially more common in journals based in North America compared with Europe. Further research is required to explore the implications of listing academic degrees on the readers’ attitude towards research quality.
The relationship between Helicobacter pylori infection and intestinal parasites in individuals from Khartoum state, Sudan: a case-control study
Authors: Yousif Abd Elbagi Yasir , Abd Alla Ahmed Bakheet , Saad Mohammed Baha Eldin
Published: December 2019

Background: In developing countries, Helicobacter pylori infection is common, as are intestinal parasites. Socioeconomic circumstances and low personal hygiene lead to the spread of these infections. This research aimed to evaluate the relationship between intestinal parasites and H. pylori in Khartoum, Sudan.

Methods: This study was conducted in various hospitals in Khartoum between June and October 2018. The study involved 200 individuals: 100 patients with H. pylori as a case group and 100 healthy individuals as a control group. A stool sample was taken from each individual, and wet preparation, saturated sodium chloride flotation and formal ether concentration were used to detect intestinal parasites.

Results: The results showed that 23% of H. pylori patients and 10% of healthy individuals had gastrointestinal parasites; Entamoeba histolytica was found in 12% of H. pylori cases followed by Entamoeba coli (7%) and Giardia lamblia (4%). Control group: Entamoeba histolytica in 5% followed by G. lamblia in 3% and E. coli in 2% of individuals. There was a significant difference in the prevalence of intestinal parasites between groups (P = 0.013).

The prevalence rate of intestinal parasites among men and women was 24% and 22%, respectively, in the case group, and 9% and 11%, respectively, in the control group. In the case group, the highest prevalence rates (40% and 38%) were found among the age groups 1-15 and 46-60 years old, respectively, while the lowest rate (10.7%) was found among the 31-45 age group. In the control group, the highest prevalence rate (15%) was among the 31-45 age group, the lowest prevalence rate (8%) was found among the 16-30 age group.

Conclusion: Together, we found that intestinal parasites are more common in patients with H. pylori. We also noticed that the rate of infection was not affected by gender while the age group was affected.
Invariance in ecological pattern
Authors: Frank Steven A. , Bascompte Jordi
Published: December 2019

Background: The abundance of different species in a community often follows the log series distribution. Other ecological patterns also have simple forms. Why does the complexity and variability of ecological systems reduce to such simplicity? Common answers include maximum entropy, neutrality, and convergent outcome from different underlying biological processes. 

Methods: This article proposes a more general answer based on the concept of invariance, the property by which a pattern remains the same after transformation. Invariance has a long tradition in physics. For example, general relativity emphasizes the need for the equations describing the laws of physics to have the same form in all frames of reference. 

Results: By bringing this unifying invariance approach into ecology, we show that the log series pattern dominates when the consequences of processes acting on abundance are invariant to the addition or multiplication of abundance by a constant. The lognormal pattern dominates when the processes acting on net species growth rate obey rotational invariance (symmetry) with respect to the summing up of the individual component processes.

Conclusions: Recognizing how these invariances connect pattern to process leads to a synthesis of previous approaches. First, invariance provides a simpler and more fundamental maximum entropy derivation of the log series distribution. Second, invariance provides a simple derivation of the key result from neutral theory: the log series at the metacommunity scale and a clearer form of the skewed lognormal at the local community scale. The invariance expressions are easy to understand because they uniquely describe the basic underlying components that shape pattern.
ПОЛОВЫЕ РАЗЛИЧИЯ В ПРОЯВЛЕНИИ КОММУНИКАТИВНОЙ КОМПЕТЕНТНОСТИ ЮНОШЕЙ И ДЕВУШЕК
Authors: Buvalets N. K.
Published: December 2019

В статье изучена коммуникативная компетентность юношей и девушек, которая играет важную роль в умении выстраивать благоприятные и успешные межличностные взаимоотношения друг с другом.
Pembangkitan Terahertz pada Metamaterial Chiral Menggunakan Spektroskopi Emisi Terahertz
Authors: Partini Juliasih , Widiatmono Restu
Published: December 2019

Metamaterial adalah material buatan dengan indeks bias negatif dan secara simultan memiliki permitivitas elektrik dan permeabilitas magnetik bernilai negatif. Pengembangan metamaterial mengalami terobosan dengan munculnya struktur metamaterial baru yang disebut sebagai metamaterial struktur chiral sebagai sumber radiasi terahertz (THz). Pengukuran sinyal emisi THz dilakukan menggunakan sistem spektroskopi emisi terahertz dengan sistem laser Ti:Sapphire femtosekon sebagai sumber radiasi. Sampel metamaterial chiral dengan ukuran panjang 1,2 mm, lebar 0,3 mm dan kedalaman 0,3 mm susunan 300 struktur dengan arah putar kanan dan putar kiri. Kedua sampel mampu membangkitkan emisi gelombang THz dalam jangkau frekuensi 0 - 2,24 THz. Proses rektifikasi optik diperlihatkan oleh adanya pembangkitan gelombang THz pada sampel metamaterial chiral oleh laser femtosekon. Hasil eksperimen memperoleh hubungan kuadratik antara energi laser pemompa dengan amplitudo gelombang THz. Hal ini dapat disimpulkan bahwa metamaterial chiral persegi dengan kedalaman berbeda telah berhasil membangkitkan emisi gelombang THz yang terpolarisasi eliptik.
DFT-based QSAR studies and Molecular Docking of 1-Phenylcyclohexylamine Analogues as anticonvulsant of NMDA Receptor
Authors: Hadni Hanine , EL M'Barki Charif , Mazigh Mohamed , Elhallaoui Menana
Published: December 2019

The phencyclidine (PCP) and their analogues have been reported to exhibit inhibitory activities toward the N-methyl-D-aspartate receptor (NMDAR). To discover the QSAR between structure of PCP derivatives and Ki activities we have used density functional theory (DFT) to generate quantum descriptors, multiple regression linear (MLR) method was applied to establish QSAR model, and an artificial neural network (ANN), considering the relevant descriptors obtained with the MLR method is explored, a correlation coefficient of RANN = 0.912 was obtained with 6-4-1 ANN model. This model is tested by using a cross-validation method with the LOO procedure (RCV = 0.841). To study the configuration impact on activity, we proceed to the Molecular Docking of four configurations, two configurations of compound have (Ki = 502 nM) and two configurations of compound have (Ki = 1200nM). The phenyl group, when placed in an equatorial position in cis9e, a configuration of the less active compound, does not form π-sigma interaction. The superimposition of this configuration with trans7e reveals that the phenyl group of cis9e configuration is shifted from the binding site compared to trans7e which forms an interaction π-sigma throughout its phenyl group with ARG B: 894. So, we could claim that the cis9e is the configuration adopted by compound having (Ki = 502 nM).
Detection and sensing of hemoglobin using one-dimensional binary photonic crystals comprising a defect layer
Authors: Abadla Mazen M. , Elsayed Hussein A.
Published: December 2019

Believing that the detection of hemoglobin possesses a vital role in the discovery of many diseases, we present in this work a simple method for sensing and detecting hemoglobin based on one-dimensional photonic crystals. Implementing hemoglobin as a defect layer inside the proposed photonic crystal results in a resonant peak evolving within the bandgaps. The strong dependence of these resonant peaks on concentration and the consequent refractive index are the essential bases of the detection process. The role played by these parameters together with the angle of incidence on performance and efficiency of our sensor is demonstrated. In the vicinity of the investigated results, we demonstrate the values of sensitivity, figure of merit (FOM), signal-to-noise ratio (SNR), and resolution to optimize the performance of our sensor. The numerical results show a significant effect of polarization mode on performance of this sensor. For TE polarization with an angle of incidence equal to 45°, we investigated sensitivity of167nmRIU−1, SNR of 0.23, FOM of0.63RIU−1, and resolution of 257 nm.
Mechanical test study in composites using digital holographic interferometry and optical coherence tomography simultaneously
Authors: Frausto-Rea Gloria , De la Torre-Ibarra Manuel H. , Muñoz-Huerta Rafael F. , Casillas Francisco J.
Published: December 2019

A dual optical configuration to inspect the internal and external mechanical response of a composite specimen is presented. The inspection simultaneously uses two equally aligned optical techniques, digital holographic interferometry and Fourier domain optical coherence tomography, to retrieve surface and internal data, respectively. The sample under study is a composite specimen of poly-methyl-methacrylate reinforced with metallic particles. Two different sets of samples are analyzed to compare their mechanical behavior. A homemade, fully controlled testing machine is used to apply a controlled compression load while each technique registers an image. In this form, the surface and internal optical phase measurements are correlated to the same compression value for comparison purposes. Results for each technique are directly presented as simultaneous displacement maps, and a discussion and conclusion of this proposed dual method of inspection are presented.
Impact of high UV fluences on the mechanical and sensing properties of polymer optical fibers for high strain measurements
Authors: Bonefacino Julien , Cheng Xin , Pun Chi-Fung Jeff , Boles Steven T. , Tam Hwa-Yaw
Published: December 2019

PMMA-based fibers are widely studied for strain measurements and show repeatable results for Fiber Bragg Gratings (FBGs) inscribed using 325 nm laser and 248 nm laser. However, there is no available material mechanical behavior characterization of the UV source impact on the fiber properties. In this manuscript, fibers are irradiated with high fluence of 325 nm and 248 nm lasers and the fibers properties are investigated using dynamic mechanical analysis and tensile strain for potential use of these fibers past the yield point. It is demonstrated that the UV sources shifted the ultimate tensile strength and changed the strain hardening behavior. Tensile strain measurements show excellent repeatability for gratings inscribed with these two sources with similar sensitivity of 1.305 nm/mɛ for FBG inscribe with 325 nm laser, and 1.345 nm/mɛ for grating written with 248 nm laser in the range 0 to 1.5 % elongation. Furthermore, tests far beyond the yield point (up to 2.8 % elongation) show that grating inscribed with lower UV wavelength exhibit hysteresis. Finally, we demonstrate that 248 nm laser fluence shall be chosen carefully whereas even high 325 nm laser fluence do not critically impact the sensor properties.
Ultrawide temperature range operation of SPR sensor utilizing a depressed double cladding fiber coated with Au-Polydimethylsiloxane
Authors: Yang Zhao , Xia Jianchun , Li Shiyu , Qi Ruiling , Zuo Guomeng , Li Wei
Published: December 2019

A surface plasmon resonance (SPR) temperature sensor on the basis of depressed double cladding fiber (DDCF) is theoretically proposed and experimentally demonstrated for the first time. Simulation analysis implies that the SPR fiber optic structure consisting of a multimode fiber (MMF) inserted into an 8 mm long DDCF is highly sensitive to the refractive index (RI) of the surrounding environment, owing to their mismatched cores, large discrepancy in cladding diameters, and the depressed inner cladding in DDCF. The experimental results further verify that the highest RI sensitivity is 7002 nm/RIU established with a 50nm Au coated DDCF-SPR sensor. Additionally, the temperature sensitivity reaches up to −2.27 nm/°C within a wide working temperature range of −30 to 330 °C by combining polydimethylsiloxane (PDMS) film as the temperature sensitive material with DDCF-Au architecture. The integrated PDMS, Au and DDCF temperature sensor possesses high performance in terms of sensing capability and physical construction, opening a route to their potential applications in other types of sensors.
Silver nanowires with different concentration for Q-switched fiber lasers
Authors: Liu Mengli , Liu Wenjun , Hou Huanran , Ouyang Yuyi , Lei Ming , Wei Zhiyi
Published: December 2019

Silver nanowire (AgNW) has become preferred due to its excellent performance in terms of biocompatibility, transparency, heat transfer and conductivity, and thus has been widely used in catalysts, microelectronic devices, sensors, solar cells, etc. Although some related properties of which have aroused great interest, the nonlinear optical properties of AgNW in laser have not been reported so far. In this paper, the nonlinear optical properties of AgNW are explored in Q-switched fiber laser. Additionally, the effects of three different AgNWs on the performance of corresponding Q-switched lasers are investigated. Results show that the concentration, saturation intensity, insertion loss and modulation depth of AgNW have great influence on the performance of lasers. Moreover, compared with similar SA-based lasers, the AgNW-based laser implemented has bright application prospects in the generation of ultrashort pulses.
Phonon effects in quantum dot single-photon sources
Authors: Denning Emil V. , Iles-Smith Jake , Gregersen Niels , Mork Jesper
Published: December 2019

Semiconductor quantum dots are inevitably coupled to the vibrational modes of their host lattice. This interaction reduces the efficiency and the indistinguishability of single-photons emitted from semiconductor quantum dots. While the adverse effects of phonons can be significantly reduced by embedding the quantum dot in a photonic cavity, phonon-induced signatures in the emitted photons cannot be completely suppressed and constitute a fundamental limit to the ultimate performance of single-photon sources based on quantum dots. In this paper, we present a self-consistent theoretical description of phonon effects in such sources and describe their influence on the figures of merit.
Definitive endoderm differentiation is promoted in suspension cultured human iPS-derived spheroids more than in adherent cells
Authors: Yabe Shigeharu G. , Nishida Junko , Fukuda Satsuki , Takeda Fujie , Nashiro Kiyoko , Ibuki Masato , Okochi Hitoshi
Published: December 2019

Human pluripotent stem cells (hPSCs), such as embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), are very attractive cell sources for the treatment of diabetes mellitus, because numerous cells can be obtained using their infinite proliferation potential to overcome the paucity of donor islets. Advances in differentiation protocols make it possible to generate glucose responsive hPSC-beta cells, which can ameliorate hyperglycemia in diabetic mice. These protocols have mainly been based on an adherent culture system. However, in clinical applications, suspension culture methods are more suitable for large-scale culture. There are reports that suspension culture and spheroid formation promote differentiation in various cell types, including hPSCs, but, to our knowledge, there are no reports comparing gene expression patterns between suspension and adherent cultured human iPSCs (hiPSCs) during definitive endoderm (DE) differentiation. In this study, we chose several stage marker genes, not only for DE but also for posterior epiblast and primitive streak, and we examined their time course expression in suspension and adherent cultures by quantitative PT-PCR (qPCR), western blot, flow cytometry and immunocytochemistry. Our results demonstrate that expressions of these marker genes are faster and more strongly induced in suspension culture than in adherent culture during the DE differentiation process, indicating that suspension culture favors DE differentiation.
Comparative analysis of p4ha1 and p4ha2 expression during Xenopus laevis development
Authors: Martini Davide , Giannaccini Martina , Guadagni Viviana , Marracci Silvia , Giudetti Guido , Andreazzoli Massimiliano
Published: December 2019

Collagen prolyl 4-hydroxylases (c-P4Hs) are evolutionary conserved enzymes whose activity is essential for the correct folding of stable triple helical molecules of collagen and collagen-like proteins. They play crucial roles in embryo development, connective tissue functional organization, tumor growth and metastasis. Despite the important function of these enzymes, little is known about their expression during vertebrate development. In this study, we determine and compare the previously undescribed spatio-temporal expression patterns of the p4ha1 and p4ha2 genes, which encode the main subunits containing the enzyme active site, during Xenopus development. The two genes are maternally inherited and share expression in dorsal mesoderm, branchial arches and their derivatives, as well as in the central nervous system, although with distinct spatio-temporal patterns. A major co-expression domain for p4ha1 and p4ha2 is represented by the developing notochord, where these genes are transcribed from early neurula stage to stage 42 tadpole, thus paralleling the profile of collagen II production and suggesting a coordination between collagen synthesis and its post-translational modifications.
Evolution of multicellularity in Dictyostelia
Authors: Kawabe Yoshinori , Du Qingyou , Schilde Christina , Schaap Pauline
Published: December 2019

The well-orchestrated multicellular life cycle of Dictyostelium discoideum has fascinated biologists for over a century. Self-organisation of its amoebas into aggregates, migrating slugs and fruiting structures by pulsatile cAMP signalling and their ability to follow separate differentiation pathways in well-regulated proportions continue to be topics under investigation. A striking aspect of D. discoideum development is the recurrent use of cAMP as chemoattractant, differentiation inducing signal and second messenger for other signals that control the developmental programme. D. discoideum is one of >150 species of Dictyostelia and aggregative life styles similar to those of Dictyostelia evolved many times in eukaryotes. Here we review experimental studies investigating how phenotypic complexity and cAMP signalling co-evolved in Dictyostelia. In addition, we summarize comparative genomic studies of multicellular Dictyostelia and unicellular Amoebozoa aimed to identify evolutionary conservation and change in all genes known to be essential for D. discoideum development.
Cooperation and conflict in the social amoeba Dictyostelium discoideum
Authors: Medina James M. , Shreenidhi P.M. , Larsen Tyler J. , Queller David C. , Strassmann Joan E.
Published: December 2019

The social amoeba Dictyostelium discoideum has provided considerable insight into the evolution of cooperation and conflict. Under starvation, D. discoideum amoebas cooperate to form a fruiting body comprised of hardy spores atop a stalk. The stalk development is altruistic because stalk cells die to aid spore dispersal. The high relatedness of cells in fruiting bodies in nature implies that this altruism often benefits relatives. However, since the fruiting body forms through aggregation there is potential for non-relatives to join the aggregate and create conflict over spore and stalk fates. Cheating is common in chimeras of social amoebas, where one genotype often takes advantage of the other and makes more spores. This social conflict is a significant force in nature as indicated by rapid rates of adaptive evolution in genes involved in cheating and its resistance. However, cheating can be prevented by high relatedness, allorecognition via tgr genes, pleiotropy and evolved resistance. Future avenues for the study of cooperation and conflict in D. discoideum include the sexual cycle as well as the relationship between D. discoideum and its bacterial symbionts. D. discoideum’s tractability in the laboratory as well as its uncommon mode of aggregative multicellularity have established it as a promising model for future studies of cooperation and conflict.
Nuclear envelope organization in Dictyostelium discoideum
Authors: Batsios Petros , Gräf Ralph , Koonce Michael P. , Larochelle Denis A. , Meyer Irene
Published: December 2019

The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export. The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun1, as well as with the LEM/HeH-family protein Src1. Sun1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun1 usually forms a so-called LINC complex. Two proteins with functions reminiscent of KASH-domain proteins at the outer nuclear membrane of Dictyostelium are known; interaptin which serves as an actin connector and the kinesin Kif9 which plays a role in the microtubule-centrosome connector. However, both of these lack the conserved KASH-domain. The link of the centrosome to the nuclear envelope is essential for the insertion of the centrosome into the nuclear envelope and the appropriate spindle formation. Moreover, centrosome insertion is involved in permeabilization of the mitotic nucleus, which ensures access of tubulin dimers and spindle assembly factors. Our recent progress in identifying key molecular players at the nuclear envelope of Dictyostelium promises further insights into the mechanisms of nuclear envelope dynamics.
dictyBase and the Dicty Stock Center (version 2.0) - a progress report
Authors: Fey Petra , Dodson Robert J. , Basu Siddhartha , Hartline Eric C. , Chisholm Rex L.
Published: December 2019

After serving the Dictyostelium community for many years, the first version of dictyBase (Chisholm et al., 2006; Fey et al., 2006) was in need of a decisive update. The original dictyBase software was not adaptable to more current demands such as handling the import of large-scale data from recently sequenced genomes, keeping up with changes in the Gene Ontology (GO), or handling the automatic annotation of over 20,000 new strains. Therefore, we have embarked on a complete overhaul of dictyBase. The new infrastructure will allow the introduction of new data, such as more expressive GO annotations and Dictyostelium disease orthologs. A modern user interface aims to streamline usage of the database including orders from the Dicty Stock Center (DSC). New displays will allow novel views including the combination of data in two new tools. With the underlying software infrastructure now in place, dictyBase software engineers and curators are currently adding the user interfaces, new tools and content pages for the evolving version 2.0 of dictyBase. This review highlights the emerging status of the new dictyBase, updated pages and annotations that will soon be available in the new environment, an overview of our annotation procedures, and plans to involve the community in curation efforts.
The Dictyostelium model for mitochondrial biology and disease
Authors: Pearce Xavier G. , Annesley Sarah J. , Fisher Paul R.
Published: December 2019

The unicellular slime mould Dictyostelium discoideum is a valuable eukaryotic model organism in the study of mitochondrial biology and disease. As a member of the Amoebozoa, a sister clade to the animals and fungi, Dictyostelium mitochondrial biology shares commonalities with these organisms, but also exhibits some features of plants. As such it has made significant contributions to the study of eukaryotic mitochondrial biology. This review provides an overview of the advances in mitochondrial biology made by the study of Dictyostelium and examines several examples where Dictyostelium has and will contribute to the understanding of mitochondrial disease. The study of Dictyostelium’s mitochondrial biology has contributed to the understanding of mitochondrial genetics, transcription, protein import, respiration, morphology and trafficking, and the role of mitochondria in cellular differentiation. Dictyostelium is also proving to be a versatile model organism in the study both of classical mitochondrial disease e.g. Leigh syndrome, and in mitochondria-associated neurodegenerative diseases like Parkinson’s disease. The study of mitochondrial diseases presents a unique challenge due to the cryptic nature of their genotype-phenotype relationship. The use of Dictyostelium can contribute to resolving this problem by providing a genetically tractable, haploid eukaryotic organism with a suite of readily characterised phenotype readouts of cellular signalling pathways. Dictyostelium has provided insight into the signalling pathways involved in multiple neurodegenerative diseases and will continue to provide a significant contribution to the understanding of mitochondrial biology and disease.
The endocytic pathways of Dictyostelium discoideum
Authors: Vines James H. , King Jason S.
Published: December 2019

The formation and processing of vesicles from the cell surface serves many important cellular functions ranging from nutrient acquisition to regulating the turnover of membrane components and signalling. In this article, we summarise the endocytic pathways of the social amoeba Dictyostelium from the clathrin-dependent and independent internalisation of surface components to the engulfment of bacteria or fluid by phagocytosis and macropinocytosis respectively. Due to similarities with the professional phagocytes of the mammalian immune system Dictyostelium has been extensively used to investigate the complex remodelling and trafficking events that occur as phagosomes and macropinosomes transit through the cell. Here we discuss what is known about this maturation process in order to kill any potential pathogens and obtain nutrients for growth. Finally, we aim to put these studies in evolutionary context and highlight some of the many questions that remain in our understanding of these complex and important pathways.
Integrated actions of mTOR complexes 1 and 2 for growth and development of Dictyostelium
Authors: Jaiswal Pundrik , Majithia Amit R. , Rosel Daniel , Liao Xin-Hua , Khurana Taruna , Kimmel Alan R.
Published: December 2019

Multi-protein complexes mTORC1 and mTORC2 are required for growth and development of eukaryotes. mTORC1 is a nutrient sensor that integrates metabolic signals and energy state to regulate cell growth/proliferation, whereas, mTORC2 primarily regulates developmental processes. Dictyostelium proliferate in rich growth media, but initiate development upon nutrient depletion. Both mTOR complexes play essential roles in Dictyostelium, where growth and developmental cycles independently require, respectively, mTORC1 or mTORC2. Many protein associations and regulatory pathways for mTORC1 and mTORC2 in Dictyostelium have context similarity to mammalian cells and specificity to inhibition by the immunosuppressive drug rapamycin. In Dictyostelium, mTORC1 function is inactivated upon starvation-induced development, but development is directly induced through rapamycin-mediated inhibition of mTORC1 activity, even in the absence of nutrient withdrawal. Pharmacologic inhibition of mTORC1, in the absence of nutrient loss, has allowed the identification of a class of essential up-regulated, developmentally-associated signaling genes and down-regulated, growth genes. We also review functional pathway regulations that integrate mTORC1/mTORC2 activities and emphasize complexity of small GTPase regulation of mTORC2 activity. Finally, epistases experiments have suggested novel upstream pathway cross-talk in Dictyostelium that requires mTORC1 and mTORC2, but for separate and independent downstream functions.
Actin assembly states in Dictyostelium discoideum at different stages of development and during cellular stress
Authors: Ishikawa-Ankerhold Hellen C. , Müller-Taubenberger Annette
Published: December 2019

The actin cytoskeleton of non-muscle cells is essential for cellular structure and subcellular organization, and the dynamic regulation of actin assembly and disassembly is a prerequisite for motility. Pioneering work using Dictyostelium discoideum focused on the biochemical analysis of non-muscle actin, the identification of actin-regulating proteins and their specific functions during processes like cell migration, cytokinesis, phagocytosis, and morphogenesis. Although subsequent work in higher eukaryotes revealed that the processes regulating actin dynamics are often much more complex, results obtained by using Dictyostelium have been of fundamental importance because they have contributed significantly to our understanding of the actin cytoskeleton in higher eukaryotes. Dictyostelium is an accepted model system for studying fast moving cells, because the single cells of the organism share many similarities with cells of the immune system such as human neutrophils. Here we provide a brief overview on the milestones of research of the actin cytoskeleton taking advantage of Dictyostelium. Furthermore, we summarize how actin structures and cytoskeletal dynamics at different stages of development have been visualized, and give an overview on the current focus of research. In addition, we discuss results showing actin assembly states during phases of cellular stress and how stress-induced actin assembly states may contribute to our understanding of certain diseases.
Dictyostelium as model for studying ubiquitination and deubiquitination
Authors: Pergolizzi Barbara , Bozzaro Salvatore , Bracco Enrico
Published: December 2019

By protein quality control and degradation, the ubiquitin system drives many essential regulatory processes such as cell cycle and division, signalling, DNA replication and repair. Therefore, dysfunctions in the ubiquitin system lead to many human disease states. However, despite the immense progress made over the last couple of decades, it appears that the ubiquitin system is more complex and multi-faced than formerly expected. In addition to a rich repertoire of ubiquitin, ubiquitin conjugating and de-ubiquitylating enzymes, the social amoeba Dictyostelium discoideum genome encodes also for a wide array of ubiquitin binding domain-containing proteins, thus offering the possibility to explore the biology of the ubiquitin system from cell and molecular biology points of view. We here provide an overview on the current knowledge about the Ub-system components and we discuss how Dictyostelium might be an outstanding eukaryotic cell model for unravelling the still mostly unknown ubiquitination mechanisms of some human diseases.
The excitable signal transduction networks: movers and shapers of eukaryotic cell migration
Authors: Pal Dhiman S. , Li Xiaoguang , Banerjee Tatsat , Miao Yuchuan , Devreotes Peter N.
Published: December 2019

In response to a variety of external cues, eukaryotic cells display varied migratory modes to perform their physiological functions during development and in the adult. Aberrations in cell migration result in embryonic defects and cancer metastasis. The molecular components involved in cell migration are remarkably conserved between the social amoeba Dictyostelium and mammalian cells. This makes the amoeba an excellent model system for studies of eukaryotic cell migration. These migration-associated components can be grouped into three networks: input, signal transduction and cytoskeletal. In migrating cells, signal transduction events such as Ras or PI3K activity occur at the protrusion tips, referred to as ‘front’, whereas events such as dissociation of PTEN from these regions are referred to as ‘back’. Asymmetric distribution of such front and back events is crucial for establishing polarity and guiding cell migration. The triggering of these signaling events displays properties of biochemical excitability including all-or-nothing responsiveness to suprathreshold stimuli, refractoriness, and wave propagation. These signal transduction waves originate from a point and propagate towards the edge of the cell, thereby driving cytoskeletal activity and cellular protrusions. Any change in the threshold for network activation alters the range of the propagating waves and the size of cellular protrusions which gives rise to various migratory modes in cells. Thus, this review highlights excitable signal transduction networks as key players for coordinating cytoskeletal activities to drive cell migration in all eukaryotes.
HERMENÊUTICA FILOSÓFICA: O CONCEITO DE EXPERIÊNCIA COMO CONTRIBUIÇÃO PARA O FORTALECIMENTO DA EDUCAÇÃO AMBIENTAL
Authors: Zambam Rodrigo Eder , Calloni Humberto
Published: December 2019

A fim de que possamos compreender minimamente a influência que a ciência moderna possui na crise socioambiental, objetivamos problematizar o conceito de “experiência” como base do projeto moderno de conhecimento e sua influência na educação tradicional. Em outra entrada, com a Hermenêutica Filosófica de Hans-Georg Gadamer (1900-2002), propomos pensar a “experiência” em seu sentido verdadeiro, ou seja, com sua característica “negativa”: “aquela na qual o homem se torna consciente de sua finitude”. Propomos que a mesma se dê no “jogo dialógico” como possibilidade da Educação acontecer de forma coletiva.
A COLETIVIDADE EM TEMPOS TEMEROSOS: BREVE RELATO DA PARCERIA ENTRE O PPGEA/FURG E O COMDESCCON
Authors: Amaral Marcel Jardim , Pereira Vilmar Alves
Published: December 2019

Em tempos temerosos dos quais estamos vivendo, as expressões de ódio e preconceito social e racial, também se reproduzem na universidade. Neste sentido é fundamental que o corpo docente/discente fique atento, bem como reveja suas posturas e principalmente vise comprometer-se com os movimentos sociais populares e a comunidade em geral, potencializando e dialogando com os saberes para além dos muros da educação formal. A educação ambiental pode precaver-se dos problemas ainda não solucionados diante o conservadorismo e moralismo latente do presente, visto de que possui de alternativas de ação para a possibilidade de uma transformação social. Este artigo pretende relatar as experiências educacionais que estão sendo proporcionadas através da coletividade entre o PPGEA/FURG e o Conselho Municipal do Negro-COMDESCCON.
REPRESENTAÇÕES AMBIENTAIS EM MANUAIS DIDÁTICOS ELABORADOS PARA PRODUÇÃO DE HORTAS ESCOLARES
Authors: Silva Fernanda Marques da , Da Silva Pereira Elenise , Azambuja Leticia
Published: December 2019

Atividades que proporcionam a confecção de hortas nas escolas é frequente no ensino de Ciências, e também são utilizadas exaustivamente como um dos pilares da Educação Ambiental. Problematizar estas atividades realizadas e observar a confecção de uma horta nas aulas de Ciências, estimulou o objetivo desta pesquisa: a análise de manuais para confecção de hortas. A metodologia utilizada está vinculada à análise cultural problematizando as representações presentes nestes manuais, os quais, a partir dos resultados, demonstram linguagens que representam e transmitem aspectos antropocêntricos, nomeiam vegetais como úteis e não úteis, ensinam como matar insetos e moluscos. Estes resultados geraram questionamentos: É isso que queremos ensinar aos nossos alunos? Conclui-se que a prática da horta não deve ser abolida do ensino, mas sim repensada enquanto importante recurso para a Educação Ambiental.
UMA BREVE ANÁLISE DA FEIRA AGROECOLÓGICA DO PARQUE DO SABIÁ EM UBERLÂNDIA - MG
Authors: Santos Mariana Moreira , Oliveira Taynara Laís Martins de Oliveira , Bernardes Maria Beatriz Junqueira
Published: December 2019

A agroecologia tem ganhado espaço na vida de cada vez mais pessoas, tanto para produtores quanto para consumidores, na disseminação da busca por um modo de vida ecológico e uma alimentação saudável. A cidade de Uberlândia – MG recebeu uma nova Feira Agroecológica semanal, que ocorre no Parque do Sabiá. Este trabalho tem como objetivo conhecer a trama que envolve a produção e comercialização da feira que ocorre no referido parque. Para a construção dessa análise foi realizada pesquisa bibliográfica, visita à feira e análise das informações obtidas por meio da entrevista realizada. Pôde-se perceber que existe a demanda da população uberlandense por produtos agroecológicos, e os feirantes têm percebido que o maior desafio é ter espaço no mercado. Neste caso, conquistar mais consumidores se torna um trabalho intrínseco à educação ambiental.
A EDUCAÇÃO AMBIENTAL COMO PRÁTICA PROMOTORA DE INTERAÇÃO NO CONTEXTO ESCOLAR
Authors: Chagas Priscila Wally Virissio , Noguez Janaína Amorim , Garcia Narjara Mendes
Published: December 2019

O texto em questão apresenta a análise de um projeto de Educação Ambiental desenvolvido tendo como contexto uma escola da rede municipal de Rio Grande/RS. Através da metodologia Inserção Ecológica e dos estudos teóricos da Bioecologia do Desenvolvimento Humano de Urie Bronfenbrenner (1917-2005), buscamos responder ao seguinte problema de pesquisa: Ao estabelecer os conceitos proximais de Reciprocidade e Afetividade nas práticas de Educação Ambiental na escola, educadores e educandos estabelecem Díades promotoras de desenvolvimento humano? Desta forma, emerge ainda, a discussão conceitual sobre o princípio de Pertencimento como fundamental na constituição de projetos de Educação Ambiental no ambiente escolar, tendo como conclusão que tais ações fazem emergir a reciprocidade e a afetividade na relação professor-aluno.
A CONSTRUÇÃO DO SER DOCENTE NUMA PERSPECTIVA COSMOCENA
Authors: Couto Andréia Martins do , Malta Marcia Madeira , Gelato Tatiele Roehrs
Published: December 2019

O presente estudo bibliográfico apresenta um diálogo reflexivo sobre a constituição do ser docente na perspectiva da Pedagogia Cosmocena, busca compreender quais as contribuições da Pedagogia Cosmocena na construção do docente. Ressalta por meio de um olhar compreensivo hermenêutico possibilidades de atuação docente para além da dimensão técnica. O estudo contribui para a ampliação de pressupostos epistemológicos da didática que abranjam a dimensão humana, questionando a racionalidade instrumental muitas vezes presentes na constituição do ser docente. Assim, possibilitando outras formas de conceber os processos vinculados ao âmbito da Educação, a Pedagogia Cosmocena instiga a busca por novas metodologias de ensino, concepções de avaliação, propostas didáticas e, sobretudo, outras epistemologias à constituição docente.