bluuebunny/crossref_metadata_2025 huggingface dataset:
Skeletal Muscle Contraction Time and Tone Decrease After 8 Weeks of Plyometric Training
Authors: Zubac Damir , Šimunič Boštjan
Published: October 2016

Zubac, D and Šimunič, B. Skeletal muscle contraction time and tone decrease after 8 weeks of plyometric training. J Strength Cond Res 31(6): 1610–1619, 2017—The aim of the study was to examine whether an improvement in jumping performance after 8 weeks of plyometric training (PT) runs in parallel with changes in lower-limb skeletal muscle contractile properties. Using noninvasive tensiomyography (TMG), we assessed contraction time (Tc) and the maximal amplitude of radial displacement (Dm) in 20 subjects (50% men; age 22.4 ± 4.7 years of age), randomly divided in PT group (N = 10; PLYO) and a control group (N = 10; CTRL). The PLYO performed 8 weeks of PT. Tensiomyography was measured in 5 leg skeletal muscles: vastus lateralis (VL), biceps femoris (BF), tibialis anterior (TA), gastrocnemius medialis (GM), and gastrocnemius lateralis (GL). Additionally, we evaluated countermovement jump (CMJ) height improvement on a ground force plate. Assessments were repeated before and after PT. After 8 weeks of PT, CMJ height increased by 12.2% in PLYO (p = 0.015), but not in CRTL. Contraction time, which is related to myosin heavy-chain type 1 (MHC-1) proportion, decreased in VL (−8.7%; p < 0.001), BF (−26.7%; p = 0.032), TA (−32.9%; p = 0.004), and GL (−25.8%; p = 0.044), but not in GM (−8.1%; p = 0.158). The estimated VL MHC-1 proportion decreased by −8.2% (p = 0.041). The maximal amplitude of radial displacement, inversely related to muscle tone, decreased in BF (−26.5%; p = 0.032), GM (−14.9%; p = 0.017), GL (−31.5%; p = 0.017), but not in TA (−16.8%; p = 0.113) and VL (−6.0%; p = 0.654). After PT, jumping performance increased, which was paralleled by decreased Tc and decreased muscle tone. Additionally, adaptations to contractile properties were muscle specific, which is important for future studies. It seems that adjustments were dose dependent, being higher in muscles with lower habitual load.
Effect of Lower-Body Resistance Training on Upper-Body Strength Adaptation in Trained Men
Authors: Bartolomei Sandro , Hoffman Jay R. , Stout Jeffrey R. , Merni Franco
Published: October 2016

Bartolomei, S, Hoffman, JR, Stout, JR, and Merni, F. Effect of lower-body resistance training on upper-body strength adaptation in trained men. J Strength Cond Res 32(1): 13–18, 2018—The aim of this study was to examine the effect of 2 different lower-body strength training schemes on upper-body adaptations to resistance training. Twenty resistance-trained men (4.25 ± 1.6 years of experience) were randomly assigned to either a high intensity (HI; n = 9; age = 24.9 ± 2.9 years; body mass = 88.7 ± 17.2 kg; height = 177.0 ± 5.6 cm) or a mixed high volume and HI resistance training program (MP; n = 11; age = 26.0 ± 4.7 years; body mass = 82.8 ± 9.1 kg; height = 177.54 ± 5.9 cm). High-intensity group followed a HI training for both upper and lower body (4–5 reps at 88%–90% of 1 repetition maximum (1RM)), whereas the MP group performed high-volume training sessions focused on muscle hypertrophy for lower body (10–12 reps at 65%–70% of 1-RM) and a HI protocol for the upper body. Maximal strength and power testing occurred before and after the 6-week training program. Analysis of covariance was used to compare performance measures between the groups. Greater increases in MP groups compared with HI groups were observed for bench press 1RM (p = 0.007), bench press power at 50% of 1RM (p = 0.011), and for arm muscle area (p = 0.046). Significant difference between the 2 groups at posttest were also observed for fat mass (p = 0.009). Results indicated that training programs focused on lower-body muscle hypertrophy and maximal strength for upper body can stimulate greater strength and power gains in the upper body compared with HI resistance training programs for both the upper and lower body.
Spiritual Activism, Visionary Pragmatism, and Threshold Theorizing
Authors: Keating AnaLouise
Published: October 2016

Focusing on explorations of spirituality in Gloria Anzaldúa's theory of spiritual activism and Patricia Hill Collins's theory of visionary pragmatism, this forum essay invites scholars of black feminist thought to explore Anzaldúa's work and include it in their research specialties. This meditation models “threshold theorizing” as a dialogic method enabling additional angles of vision and thus generating new, potentially provocative, and transformative insights. It also demonstrates the value of spirituality and spiritual activism to contemporary research.
Black Feminist Thought as Methodology
Authors: Patterson Ashley , Kinloch Valerie , Burkhard Tanja , Randall Ryann , Howard Arianna
Published: October 2016

In this essay, we rely on a black feminist lens to challenge and extend what is appraised as rigorous research methodology. Inspired by a diverse, intergenerational group of black women referred to as the Black Women's Gathering Place, we employ black feminist thought (BFT) as critical social theory and embrace a more expansive understanding of BFT as critical methodology to analyze the experiences black women share through narrative. Our theoretical and methodological approach offers a pathway for education and research communities to account for the expansive possibilities that black feminism has for theorizing the lives of black women.
Retrotransposon Proliferation Coincident with the Evolution of Dioecy inAsparagus
Authors: Harkess Alex , Mercati Francesco , Abbate Loredana , McKain Michael , Pires J Chris , Sala Tea , Sunseri Francesco , Falavigna Agostino , Leebens-Mack Jim
Published: October 2016

Current phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once, or possibly twice, in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n = 2× = 20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here, we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion, or to retrotransposon proliferation in dioecious species. We first estimate genome sizes, or use published values, for four hermaphrodites and four dioecious species distributed across the phylogeny, and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach, we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication (WGD) event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing, and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements, in particular, have undergone a marked proliferation in dioecious species. In the absence of a detectable WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species.
Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton
Authors: Shang Lianguang , Wang Yumei , Wang Xiaocui , Liu Fang , Abduweli Abdugheni , Cai Shihu , Li Yuhua , Ma Lingling , Wang Kunbo , Hua Jinping
Published: October 2016

Cotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.
Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family inSolanum lycopersicum(cv. Heinz 1706)
Authors: Krsticevic Flavia J , Arce Débora P , Ezpeleta Joaquín , Tapia Elizabeth
Published: October 2016

In plants, fruit maturation and oxidative stress can induce small heat shock protein (sHSP) synthesis to maintain cellular homeostasis. Although the tomato reference genome was published in 2012, the actual number and functionality of sHSP genes remain unknown. Using a transcriptomic (RNA-seq) and evolutionary genomic approach, putative sHSP genes in the Solanum lycopersicum (cv. Heinz 1706) genome were investigated. A sHSP gene family of 33 members was established. Remarkably, roughly half of the members of this family can be explained by nine independent tandem duplication events that determined, evolutionarily, their functional fates. Within a mitochondrial class subfamily, only one duplicated member, Solyc08g078700, retained its ancestral chaperone function, while the others, Solyc08g078710 and Solyc08g078720, likely degenerated under neutrality and lack ancestral chaperone function. Functional conservation occurred within a cytosolic class I subfamily, whose four members, Solyc06g076570, Solyc06g076560, Solyc06g076540, and Solyc06g076520, support ∼57% of the total sHSP RNAm in the red ripe fruit. Subfunctionalization occurred within a new subfamily, whose two members, Solyc04g082720 and Solyc04g082740, show heterogeneous differential expression profiles during fruit ripening. These findings, involving the birth/death of some genes or the preferential/plastic expression of some others during fruit ripening, highlight the importance of tandem duplication events in the expansion of the sHSP gene family in the tomato genome. Despite its evolutionary diversity, the sHSP gene family in the tomato genome seems to be endowed with a core set of four homeostasis genes: Solyc05g014280, Solyc03g082420, Solyc11g020330, and Solyc06g076560, which appear to provide a baseline protection during both fruit ripening and heat shock stress in different tomato tissues.
Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish
Authors: Zhong Zaixuan , Du Kang , Yu Qian , Zhang Yong E , He Shunping
Published: October 2016

The evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.
Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates inSaccharomyces cerevisiae
Authors: Neymotin Benjamin , Ettorre Victoria , Gresham David
Published: October 2016

Degradation of mRNA contributes to variation in transcript abundance. Studies of individual mRNAs have shown that both cis and trans factors affect mRNA degradation rates. However, the factors underlying transcriptome-wide variation in mRNA degradation rates are poorly understood. We investigated the contribution of different transcript properties to transcriptome-wide degradation rate variation in the budding yeast, Saccharomyces cerevisiae, using multiple regression analysis. We find that multiple transcript properties are significantly associated with variation in mRNA degradation rates, and that a model incorporating these properties explains ∼50% of the genome-wide variance. Predictors of mRNA degradation rates include transcript length, ribosome density, biased codon usage, and GC content of the third position in codons. To experimentally validate these factors, we studied individual transcripts expressed from identical promoters. We find that decreasing ribosome density by mutating the first translational start site of a transcript increases its degradation rate. Using coding sequence variants of green fluorescent protein (GFP) that differ only at synonymous sites, we show that increased GC content of the third position of codons results in decreased rates of mRNA degradation. Thus, in steady-state conditions, a large fraction of genome-wide variation in mRNA degradation rates is determined by inherent properties of transcripts, many of which are related to translation, rather than specific regulatory mechanisms.
Simple and Efficient Targeting of Multiple Genes Through CRISPR-Cas9 in Physcomitrella patens
Authors: Lopez-Obando Mauricio , Hoffmann Beate , Géry Carine , Guyon-Debast Anouchka , Téoulé Evelyne , Rameau Catherine , Bonhomme Sandrine , Nogué Fabien
Published: October 2016

Powerful genome editing technologies are needed for efficient gene function analysis. The CRISPR-Cas9 system has been adapted as an efficient gene-knock-out technology in a variety of species. However, in a number of situations, knocking out or modifying a single gene is not sufficient; this is particularly true for genes belonging to a common family, or for genes showing redundant functions. Like many plants, the model organism Physcomitrella patens has experienced multiple events of polyploidization during evolution that has resulted in a number of families of duplicated genes. Here, we report a robust CRISPR-Cas9 system, based on the codelivery of a CAS9 expressing cassette, multiple sgRNA vectors, and a cassette for transient transformation selection, for gene knock-out in multiple gene families. We demonstrate that CRISPR-Cas9-mediated targeting of five different genes allows the selection of a quintuple mutant, and all possible subcombinations of mutants, in one experiment, with no mutations detected in potential off-target sequences. Furthermore, we confirmed the observation that the presence of repeats in the vicinity of the cutting region favors deletion due to the alternative end joining pathway, for which induced frameshift mutations can be potentially predicted. Because the number of multiple gene families in Physcomitrella is substantial, this tool opens new perspectives to study the role of expanded gene families in the colonization of land by plants.
Sequential Turnovers of Sex Chromosomes in African Clawed Frogs (Xenopus) Suggest Some Genomic Regions Are Good at Sex Determination
Authors: Furman Benjamin L S , Evans Ben J
Published: October 2016

Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of African clawed frogs (genus Xenopus). Here, we extend these discoveries by demonstrating that yet another sex determination system exists in Xenopus, specifically in the species Xenopus borealis. This system evolved recently in an ancestor of X. borealis that had the same sex determination system as X. laevis, a system which itself is newly evolved. Strikingly, the genomic region carrying the sex determination factor in X. borealis is homologous to that of therian mammals, including humans. Our results offer insights into how the genetic underpinnings of conserved phenotypes evolve, and suggest an important role for cooption of genetic building blocks with conserved developmental roles.
The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition
Authors: Luo Hua , Li Xiao , Claycomb Julie M , Lipshitz Howard D
Published: October 2016

Metazoan embryos undergo a maternal-to-zygotic transition (MZT) during which maternal gene products are eliminated and the zygotic genome becomes transcriptionally active. During this process, RNA-binding proteins (RBPs) and the microRNA-induced silencing complex (miRISC) target maternal mRNAs for degradation. In Drosophila, the Smaug (SMG), Brain tumor (BRAT), and Pumilio (PUM) RBPs bind to and direct the degradation of largely distinct subsets of maternal mRNAs. SMG has also been shown to be required for zygotic synthesis of mRNAs and several members of the miR-309 family of microRNAs (miRNAs) during the MZT. Here, we have carried out global analysis of small RNAs both in wild-type and in smg mutants. Our results show that 85% of all miRNA species encoded by the genome are present during the MZT. Whereas loss of SMG has no detectable effect on Piwi-interacting RNAs (piRNAs) or small interfering RNAs (siRNAs), zygotic production of more than 70 species of miRNAs fails or is delayed in smg mutants. SMG is also required for the synthesis and stability of a key miRISC component, Argonaute 1 (AGO1), but plays no role in accumulation of the Argonaute family proteins associated with piRNAs or siRNAs. In smg mutants, maternal mRNAs that are predicted targets of the SMG-dependent zygotic miRNAs fail to be cleared. BRAT and PUM share target mRNAs with these miRNAs but not with SMG itself. We hypothesize that SMG controls the MZT, not only through direct targeting of a subset of maternal mRNAs for degradation but, indirectly, through production and function of miRNAs and miRISC, which act together with BRAT and/or PUM to control clearance of a distinct subset of maternal mRNAs.
Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton
Authors: Shang Lianguang , Ma Lingling , Wang Yumei , Su Ying , Wang Xiaocui , Li Yuhua , Abduweli Abdugheni , Cai Shihu , Liu Fang , Wang Kunbo , Hua Jinping
Published: October 2016

Plant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL) mapping at multiple developmental stages using two recombinant inbred lines (RILs) and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton.
Determinants in the LIN-12/Notch Intracellular Domain That Govern Its Activity and Stability DuringCaenorhabditis elegansVulval Development
Authors: Deng Yuting , Greenwald Iva
Published: October 2016

Upon ligand binding, the LIN-12/Notch intracellular domain is released from its transmembrane tether to function in a nuclear complex that activates transcription of target genes. During Caenorhabditis elegans vulval development, LIN-12/Notch is activated by ligand in two of six multipotential vulval precursor cells (VPCs), specifying the “secondary vulval fate” and descendants that contribute to the vulva. If LIN-12 is ectopically activated in other VPCs, they also adopt the secondary fate, dividing to produce extra vulval cells, resulting in a “Multivulva” phenotype. Here, we identify determinants in the LIN-12 intracellular domain [“LIN-12(intra)”] that govern its activity and stability during C. elegans vulval development; we assayed activity of mutant forms based on their ability to cause a Multivulva phenotype and stability using a GFP tag to visualize their accumulation. Our analysis has revealed that, while the ubiquitin ligase SEL-10/Fbw7 promotes LIN-12(intra) downregulation in VPCs, there is a distinct mechanism for downregulation of LIN-12(intra) in VPC descendants. Our analysis also revealed that LIN-12(intra) must be in the nuclear complex to be regulated appropriately in VPCs and their descendants, and that the structure or conformation of the carboxy-terminal region influences stability as well. Although activity and stability are generally well-correlated, exceptions where they are uncoupled suggest that there may be roles for the carboxy-terminal region and sel-10 that are independent of their roles in regulating LIN-12(intra) stability.
Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis
Authors: Zeman Igor , Neboháčová Martina , Gérecová Gabriela , Katonová Kornélia , Jánošíková Eva , Jakúbková Michaela , Centárová Ivana , Dunčková Ivana , Tomáška L'ubomír , Pryszcz Leszek P , Gabaldón Toni , Nosek Jozef
Published: October 2016

The pathogenic yeast Candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. The orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. Our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exception of the mitochondrially targeted 3-oxoadipate CoA-transferase (Osc1p) and 3-oxoadipyl-CoA thiolase (Oct1p) catalyzing the last two reactions of the 3-oxoadipate pathway. The cellular localization of the enzymes indicates that degradation of hydroxyaromatic compounds requires a shuttling of intermediates, cofactors, and products of the corresponding biochemical reactions between cytosol and mitochondria. Indeed, we found that yeast cells assimilating hydroxybenzoates increase the expression of genes SFC1, LEU5, YHM2, and MPC1 coding for succinate/fumarate carrier, coenzyme A carrier, oxoglutarate/citrate carrier, and the subunit of pyruvate carrier, respectively. A phylogenetic analysis uncovered distinct evolutionary trajectories for sparsely distributed gene clusters coding for enzymes of both pathways. Whereas the 3-oxoadipate pathway appears to have evolved by vertical descent combined with multiple losses, the gentisate pathway shows a striking pattern suggestive of horizontal gene transfer to the evolutionarily distant Mucorales.
Advances in Understanding Mating Type Gene Organization in the Mushroom-Forming FungusFlammulina velutipes
Authors: Wang Wei , Lian Lingdan , Xu Ping , Chou Tiansheng , Mukhtar Irum , Osakina Aron , Waqas Muhammad , Chen Bingzhi , Liu Xinrui , Liu Fang , Xie Baogui , van Peer Arend F
Published: October 2016

The initiation of sexual development in the important edible and medicinal mushroom Flammulina velutipes is controlled by special genes at two different, independent, mating type (MAT) loci: HD and PR. We expanded our understanding of the F. velutipes mating type system by analyzing the MAT loci from a series of strains. The HD locus of F. velutipes houses homeodomain genes (Hd genes) on two separated locations: sublocus HD-a and HD-b. The HD-b subloci contained strain-specific Hd1/Hd2 gene pairs, and crosses between strains with different HD-b subloci indicated a role in mating. The function of the HD-a sublocus remained undecided. Many, but not all strains contained the same conserved Hd2 gene at the HD-a sublocus. The HD locus usually segregated as a whole, though we did detect one new HD locus with a HD-a sublocus from one parental strain, and a HD-b sublocus from the other. The PR locus of F. velutipes contained pheromone receptor (STE3) and pheromone precursor (Pp) genes at two locations, sublocus PR-a and PR-b. PR-a and PR-b both contained sets of strain-specific STE3 and Pp genes, indicating a role in mating. PR-a and PR-b cosegregated in our experiments. However, the identification of additional strains with identical PR-a, yet different PR-b subloci, demonstrated that PR subloci can recombine within the PR locus. In conclusion, at least three of the four MAT subloci seem to participate in mating, and new HD and PR loci can be generated through intralocus recombination in F. velutipes.
A Pedigree-Based Map of Recombination in the Domestic Dog Genome
Authors: Campbell Christopher L , Bhérer Claude , Morrow Bernice E , Boyko Adam R , Auton Adam
Published: October 2016

Meiotic recombination in mammals has been shown to largely cluster into hotspots, which are targeted by the chromatin modifier PRDM9. The canid family, including wolves and dogs, has undergone a series of disrupting mutations in this gene, rendering PRDM9 inactive. Given the importance of PRDM9, it is of great interest to learn how its absence in the dog genome affects patterns of recombination placement. We have used genotypes from domestic dog pedigrees to generate sex-specific genetic maps of recombination in this species. On a broad scale, we find that placement of recombination events in dogs is consistent with that in mice and apes, in that the majority of recombination occurs toward the telomeres in males, while female crossing over is more frequent and evenly spread along chromosomes. It has been previously suggested that dog recombination is more uniform in distribution than that of humans; however, we found that recombination in dogs is less uniform than in humans. We examined the distribution of recombination within the genome, and found that recombination is elevated immediately upstream of the transcription start site and around CpG islands, in agreement with previous studies, but that this effect is stronger in male dogs. We also found evidence for positive crossover interference influencing the spacing between recombination events in dogs, as has been observed in other species including humans and mice. Overall our data suggests that dogs have similar broad scale properties of recombination to humans, while fine scale recombination is similar to other species lacking PRDM9.
Non-Mendelian Dominant Maternal Effects Caused by CRISPR/Cas9 Transgenic Components inDrosophila melanogaster
Authors: Lin Chun-Chieh , Potter Christopher J
Published: October 2016

The CRISPR/Cas9 system has revolutionized genomic editing. The Cas9 endonuclease targets DNA via an experimentally determined guide RNA (gRNA). This results in a double-strand break at the target site . We generated transgenic Drosophila melanogaster in which the CRISPR/Cas9 system was used to target a GAL4 transgene in vivo. To our surprise, progeny whose genomes did not contain CRISPR/Cas9 components were still capable of mutating GAL4 sequences. We demonstrate this effect was caused by maternal deposition of Cas9 and gRNAs into the embryo, leading to extensive GAL4 mutations in both somatic and germline tissues. This serves as a cautionary observation on the effects of maternal contributions when conducting experiments using genomically encoded CRISPR/Cas9 components. These results also highlight a mode of artificial inheritance in which maternal contributions of DNA editing components lead to transmissible mutant defects even in animals whose genomes lack the editing components. We suggest calling this a dominant maternal effect to reflect it is caused by the gain of maternally contributed products. Models of CRISPR-mediated gene drive will need to incorporate dominant maternal effects in order to accurately predict the efficiency and dynamics of gene drive in a population.
Between Identity and Interest: Revisiting Sharia Bylaw in Current Indonesia
Authors: Garadian Endi Aulia
Published: October 2016

The emergence of sharia bylaws in several regions in Indonesia is increasingly worrisome. In many cases, they have generated socio-religious problems within society such as preventing the establishment of a house of worship and forbidding of religious activities, especially for minority sects such as Ahmadiyya and Shi’a. Furthermore, they also produce the discrimination against women. For example, in Tangerang City, a female worker was arrested by Civil Service Police Unit (Satuan Polisi Pamong Praja, Satpol PP) because she was accused of being prostitute because she returned home at night. Unfortunately, the basis of accusation is Perda Kota Tangerang No. 5, 2005.One of the prominent factors giving occasion to the emergence of those sharia bylaws is the political opportunity after the decline of Suharto’s New Order. Afterwards, the falling regime became a sign of this glitch. Ignoring the fact that they produce many problems within society, local governments still repeatedly produce sharia bylaws.DOI: 10.15408/sdi.v23i2.3672
Communal Democracy: The Social Contract and Confederalism in Rojava
Authors: Knapp Michael , Jongerden Joost
Published: October 2016

The article engages with the question of self-governance and its implications for the concept of citizenship in Rojava. A short overview of the historical development of the political idea of democratic autonomy applied in Rojava is given, a model that claims to be on the way to creating a stateless model of radical democracy whose realisation involves forms of emancipation of the citizen, from a subject of a state to an active participant. The social contract and the structure of self-governance in Rojava is examined from this perspective, and the conclusion drawn that citizenship, which has been seized by the statist model, is currently being reclaimed by the people in Rojava through democratic autonomy. The process of change of citizenship is being effected through participative action and self-education as acts of citizenship and aims to separate the idea of government from the idea of the state.
ADRENALINO KONCENTRACIJOS VIETINIO ANESTETIKO TIRPALE ĮTAKA PACIENTO HEMODINAMIKAI TAIKANT BENDRĄJĄ NEJAUTRĄ
Authors: Činčikas Darius , Skaisgirys Karolis , Audzijonis Mindaugas
Published: October 2016

Reikšminiai žodžiai: adrenalinas, anestezija, hemodinamikos rodikliai. Darbo tikslas. Palyginti vietinei audinių infiltracijai naudojamo lidokaino tirpalo su skirtinga adrenalino koncentracija poveikį paciento hemodinamikai taikant bendrąją nejautrą. Tyrimo medžiaga ir metodai. Į randomizuotą prospektyvinį tyrimą įtraukta 30 pacientų, kuriems taikant bendrąją nejautrą atliktos nosies pertvaros plastikos operacijos. I grupei (n = 15) pacientų į pertvaros gleivinę infiltruota lidokaino tirpalo su 1:100 000 adrenalino koncentracija, II grupei (n = 15) – 1:200 000 adrenalino koncentracijos lidokaino tirpalo. Prieš atliekant injekciją (bazinis dydis) ir septynias minutes po injekcijos, kas minutę matuotas pacientų vidurinis arterinis kraujo spaudimas ir širdies susitraukimų dažnis, registruoti ritmo sutrikimų atvejai. Rezultatai. I grupėje po tirpalo injekcijos nustatytas statistiškai reikšmingas vidurinio arterinio kraujo spaudimo padidėjimas, palyginti su bazine reikšme (p = 0,005). II grupės pacientams statistiškai reikšmingų vidurinio arterinio kraujo spaudimo pokyčių (palyginti su bazine reikšme) nenustatyta. Palyginus I ir II grupes, nustatyti reikšmingi vidurinio arterinio kraujo spaudimo skirtumai 1 min. (p = 0,02), 2 min. (p = 0,001) ir 3 min. (p = 0,018). Širdies susitraukimų dažnis reikšmingai kito, tačiau tarpusavyje, tarp I ir II grupių pacientų, statistiškai patikimai nesiskyrė. Išvados. Vietiškai į nosies pertvaros gleivinę infiltruotas lidokaino su didesne adrenalino koncentracija (1:100 000) tirpalas sukėlė statistiškai reikšmingą vidurinio arterinio kraujo spaudimo padidėjimą. Lidokaino tirpalas su mažesne adrenalino koncentracija (1:200 000) nesukėlė statistiškai reikšmingų vidurinio arterinio kraujo spaudimo svyravimų. Abiejų adrenalino koncentracijų tirpalai reikšmingai įtakojo širdies susitraukimų dažnį. Visi reikšmingi hemodinamikos rodiklių pokyčiai įvyko per pirmąsias 4 min. nuo tirpalo injekcijos.
TRIUKŠMO SUKELTŲ KLAUSOS SUTRIKIMŲ ANKSTYVA DIAGNOSTIKA TAIKANT TONINĘ RIBINĘ IR YPAČ AUKŠTŲ DAŽNIŲ AUDIOMETRIJĄ
Authors: Valiūnaitė Gabrielė , Vaitkūnaitė Donata , Vainutienė Vija
Published: October 2016

Reikšminiai žodžiai: toninė ribinė audiometrija, ypač aukštų dažnių audiometrija, klausos sutrikimas, triukšmas. Darbo tikslas. Įvertinti trumpos triukšmo ekspozicijos įtaką klausos sutrikimų atsiradimui naudojant toninę ribinę ir ypač aukštų dažnių audiometriją. Tyrimo medžiaga ir metodai. Tyrime dalyvavo 20 studentų (tirta 40 ausų). Tiriamiesiems atliktos toninė ribinė (0,125–8 kHz) ir ypač aukštų dažnių (8–16 kHz) audiometrijos: prieš ir per 24 val. po triukšmo (110–125 dB) ekspozicijos. Atlikta anketinė apklausa iš 18 klausimų. Statistiniai skaičiavimai atlikti „Microsoft Excel“ programa. Rezultatai. Tirta 45 proc. vaikinų, 55 proc. merginų, vidutinis amžius – 23,2±1,3 metų. Ypač aukštų dažnių audiometrijos klausos slenksčių vidurkiai: prieš triukšmą 10,8 ± 14,8 dB, po triukšmo 12,6 ± 13,5 dB (p < 0,05). Daugiau nei 3 valandas triukšme praleidusių asmenų (40 proc.) ypač aukštų dažnių audiometrijos rezultatų vidurkiai: prieš triukšmą 5,4 ± 9,9 dB, po triukšmo 7,7 ± 9,4 dB, (p < 0,05). Moterims pastebėtas klausos pablogėjimas 8–16 kHz diapazone (prieš triukšmą 10,6 ± 14,9 dB, po triukšmo 13 ± 13,8 dB) (p < 0,05). Vyrų ypač aukštų dažnių klausos slenksčių vidurkiai: prieš triukšmą 11 ± 14 dB, po triukšmo 12,1 ± 13,3 dB (p > 0,05). Po triukšmo ekspozicijos 65 proc. studentų jautė subjektyvius klausos sutrikimus. Jiems 8–16 kHz dažniuose pastebėtas klausos slenksčių pakilimas (p < 0,05): prieš triukšmą 11,7 ± 16,1 dB, po triukšmo 13,5 ± 15 dB. Išvados. Ypač aukštų dažnių audiometrijos metodu nustatytas statistiškai patikimas klausos pablogėjimas po trumpos triukšmo ekspozicijos. Toninėje ribinėje audiometrijoje statistiškai patikimų klausos slenksčio pokyčių nebuvo rasta. Daugiau nei 3 valandas triukšme praleidusių asmenų klausos slenksčių pokyčio intervalai ypač aukštų dažnių diapazone yra didesni nei buvusių trumpiau. Moterims pastebimas ryškesnis klausos pablogėjimas nei vyrams. Asmenims, subjektyviai jautusiems klausos sutrikimus po triukšmo, audiometrinio tyrimo metu buvo nustatytas klausos slenksčio pakilimas.
STAPHYLOCOCCUS AUREUS NEŠIOJIMAS TARP VILNIAUS UNIVERSITETO MEDICINOS FAKULTETO PIRMO KURSO STUDENTŲ, ATSPARUMAS ANTIMIKROBINIAMS VAISTAMS IR NEŠIOJIMO RIZIKOS VEIKSNIŲ TYRIMAS
Authors: Kirkliauskienė Agnė , Ginčaitė Alvita , Balkutė Deimilė
Published: October 2016

Reikšminiai žodžiai: Staphylococcus aureus, nešiojimas, MASA, atsparumas antimikrobiniams vaistams. Tikslas. Nustatyti S. aureus nešiotojus tarp VU MF pirmo kurso studentų ir įvertinti galimus S. aureus nešiojimo rizikos veiksnius bei išskirtų padermių atsparumą kai kurioms antimikrobinėms medžiagoms. Metodika. Siekiant nustatyti S. aureus nešiotojus, imti mėginiai iš nosies ir ryklės. Išskirtos padermės identifikuotos taikant standartinius mikrobiologinius metodus. Rizikos veiksniams įvertinti naudota anoniminė, iš galimų S. aureus nešiojimo rizikos veiksnių sudaryta anketa. Išskirtų padermių atsparumas kai kurioms antimikrobinėms medžiagoms ištirtas laikantis Klinikinių laboratorinių standartų instituto rekomendacijų. Rezultatai. Ištirti 245 VU MF pirmo kurso studentai, paimta 490 mėginių. Nustatyta, kad 112 (45,7 proc.) respondentų yra S. aureus nešiotojai. Iš 112 nešiotojų 33 (29,5 proc.) tiriamiesiems S. aureus išskirta iš nosies, 52 (46,4 proc.) – iš ryklės, o 27 (11 proc.) asmenims – iš nosies ir ryklės. S. aureus nešiotojų vyrų (58,3 proc.) buvo daugiau nei nešiotojų moterų (40,5 proc.). Nustatytas statistiškai patikimas ryšys tarp S. aureus nešiojimo ir vyriškos lyties (ŠS = 2,06, PI 95 proc. 1,14–3,75, p = 0,008), gyvenimo su 15–25 m. asmenimis (ŠS = 1,76, PI 95 proc. 1,01–3,04, p = 0,037) ir tiriamųjų sirgimo kvėpavimo takų alerginėmis ligomis (ŠS = 3,22, PI 95 proc. 1,20–9,53, p = 0,016). Išskirtos 139 S. aureus padermės. Iš jų, remiantis išplėstine antibiotikograma, identifikuota 119 fenotipiškai skirtingų izoliuotų padermių. Nustatyta, kad 64,7 proc. išskirtų padermių atsparios penicilinui. Mažesnis atsparumo dažnis rastas tetraciklinui ir klindamicinui (5,04 proc.), eritromicinui, ciprofloksacinui ir fuzidino rūgščiai (1,68 proc.). Įvertinta, kad 20,16 proc. S. aureus padermių yra vidutiniškai atsparios streptomicinui. Visos išskirtos S. aureus padermės buvo jautrios oksacilinui/cefoksitinui, rifampinui, kanamicinui, norfloksacinui, gentamicinui ir vankomicinui. Išvados. 45,7 proc. VU MF pirmo kurso studentų yra S. aureus nešiotojai. Nustatyta, kad viršutinių kvėpavimo takų kolonizacijai S. aureus darantys įtaką rizikos veiksniai yra lytis, gyvenimas su 15–25 m. asmenimis ir alerginės ligos. Išskirtų padermių atsparumas antimikrobinėms medžiagoms nėra didelis.
TINKLAINĖS ATŠOKOS RIZIKOS VEIKSNIAI PO KATARAKTOS OPERACIJŲ
Authors: Pajėda Adomas , Pakulienė Giedrė , Pajėda Pijus , Miliauskas Arūnas , Kuzmienė Loreta
Published: October 2016

Reikšminiai žodžiai: katarakta, tinklainės atšoka, chirurgija, rizikos veiksniai. Tikslas. Įvertinti tinklainės atšokos po kataraktos operacijos rizikos veiksnių dažnį. Tyrimo medžiaga ir metodai. Atliktas retrospektyvus pacientų, operuotų dėl tinklainės atšokos (TA) po kataraktos operacijų (pseudofakinių TA), tyrimas. Surinkti šie duomenys: amžius, lytis, operuota akis, laikas nuo kataraktos pašalinimo iki TA, kataraktos operacijos metu įvykusios komplikacijos (lęšiuko saitų, priekinės ir užpakalinės kapsulės pažeidimas), akies ašies ilgis (AI), gretutinės akių ligos (trumparegystė, periferinė tinklainės degeneracija). Rezultatai. Ištirti 119 pacientų: 61,3 proc. vyrų, 38,7 proc. moterų, amžiaus vidurkis – 62,4 ± 10,9 metų. Pacientų iki 49 m. buvo mažiau nei kitose amžiaus grupėse (p < 0,01). 47,2 proc. pacientų TA išsivystė per dvejus metus po kataraktos operacijos. 49,6 proc. pacientų buvo trumparegiai, 12,6 proc. diagnozuota periferinė tinklainės degeneracija. Akių AI vidurkis 25,2 ± 2,2 mm. Daugumos pacientų akių AI buvo 23 mm arba daugiau (p < 0,05). 3,4 proc. atvejų kataraktos operacija komplikavosi užpakalinės kapsulės plyšimu, 6,7 proc. – lęšiuko saitų pažeidimu. Išvados. Pseudofakinė TA dažniau operuota vyrams ir vidutinio bei senyvo amžiaus žmonėms. Pseudofakinė TA dažniausiai išsivystė per pirmuosius 2 metus po kataraktos operacijos. Beveik pusė TA buvo trumparegėse akyse, ypač kai AI buvo daugiau nei 23 mm.
SERGANČIŲ KERATOKONUSU ILGALAIKIAI GYDYMO REZULTATAI PO RAGENOS SUSTIPRINIMO PROCEDŪROS
Authors: Socevičienė Lina , Tolutienė Vilija
Published: October 2016

Reikšminiai žodžiai: keratokonusas, ragenos sustiprinimas, ilgalaikiai rezultatai. Darbo tikslas. Įvertinti sergančių keratokonusu ilgalaikius (po 5 metų) gydymo rezultatus po ragenos sustiprinimo (CXL) procedūros. Tyrimo medžiaga ir metodai. Šio retrospektyvaus tyrimo metu vertinome keratokonusu sergančias akis, kurioms buvo atlikta ragenos sustiprinimo procedūra (CXL) Akių klinikoje „Lirema“ 2008–2010 metais. Surinkome 33 tokiu būdu gydytų akių tyrimus prieš procedūrą, 31 – po metų ir 33 – po penkerių metų po CXL. Vertinome nekoreguotą regėjimo aštrumą į tolį, geriausią korekciniais stiklais koreguotą regėjimo aštrumą į tolį (Sneleno optotipų lentelė); ragenos tomografiją („Pentacam HR, Oculus“), nustatydami maksimalią keratometrijos vertę (Kmax); endotelio ląstelių tyrimą („Tomey“, EM-3000). CXL procedūra atlikta pagal standartinį Drezdeno protokolą: pašalinus ragenos epitelį, ragenos stroma įsotinta izotoniniu 0,1 proc. riboflavino 20 proc. dekstrano tirpalu ir švitinama UVA spinduliais 5,4 J/ cm² (3,0 mW/cm² 30 min., „UV-X system“, „Peschke GmbH“). Rezultatai. Nustatytas statistiškai patikimas regėjimo aštrumo pagerėjimas visais stebėjimo laikotarpiais. Vidutinis nekoreguotas prieš gydymą 0,26 ± 0,23 po metų pagerėjo iki 0,36 ± 0,29, o po penkerių – iki 0,46 ± 0,33 (Friedmano kriterijus 32,21, Ils 2, p < 0,001). Vidutinis koreguotas prieš CXL 0,44 ± 0,23 po metų pagerėjo iki 0,6 ± 0,23 ir išliko nepakitęs tikrinant po penkerių metų 0,67 ± 0,28 (Friedmano kriterijus 35,37, Ils 2, p < 0,001). Vidutinė maksimali keratometrijos reikšmė statistiškai reikšmingai mažėja kiekvienu stebėjimo laikotarpiu: prieš procedūrą Kmax 54,72 ± 3,76D po metų sumažėjo iki Kmax 53,36 ± 3,91, o po penkerių – iki Kmax 51,84 ± 4,14D (Friedmano kriterijus 45,32, Ils 2, p < 0,001). Pastebėjome reikšmingą koreliaciją tarp nekoreguoto regėjimo aštrumo ir maksimalios keratometrijos reikšmės (r = -0,376; p = 0,031), tačiau reikšmingos koreliacijos tarp koreguoto regėjimo aštrumo ir Kmax nėra (r = -0,237; p = 0,184). Stebėjimo laikotarpiais ragenos endotelio ląstelių būklės kitimo nėra. Nenustayta jokių procedūros pašalinių ar nepageidaujamų poveikių. Išvados. Tyrimo rezultatai rodo ilgalaikį keratokonuso gydymo ragenos sustiprinimo procedūra efektyvumą. Gydant liga ne tik stabilizuojasi, bet ir regresuoja – ragenos gaubtumas mažėja, todėl pagerėja regėjimas. Tai yra saugi ir efektyvi procedūra gydyti progresuojantį keratokonusą.
PERIODONTITO IR REUMATOIDINIO ARTRITO RYŠYS. LITERATŪROS APŽVALGA
Authors: Romanova Svetlana , Žibaitė Aušra , Baranauskaitė Asta , Basevičienė Nomeda
Published: October 2016

Reikšminiai žodžiai: periodontitas, reumatoidinis artritas, P. gingivalis, citrulinacija. Darbo tikslas. Apžvelgti mokslinę literatūrą, analizuojančią periodontito ir reumatoidinio artrito patogenezinio ryšio mechanizmus. Apibendrinimas. Tyrimais nustatyta, kad periodontitas (PD) yra susijęs su kai kuriomis sisteminėmis ligomis, tarp jų – reumatoidiniu artritu (RA). Abi ligos apibūdinamos kaip lėtiniai uždegimai, kurių metu uždegiminės ląstelės ir kiti patologiniai veiksniai lemia klinikinių simptomų (patinimo, skausmo) atsiradimą ir šalia esančio kaulo destrukciją. Epidemiologiniai tyrimai patvirtina, kad PD paplitimas yra didesnis tarp RA sergančių pacientų, o ligos laipsnis – sunkesnis. Tačiau tikslus šių ligų ryšys per etiopatogenetinius mechanizmus vis dar nėra aiškus. Tyrimai nurodo abiejų lligų ryšį per autoimuninį organizmo atsaką į citrulinuotus baltymus. Daugelis RA atvejų yra inicijuoti autoimuninio atsako į citrulinuotus baltymus. Neseniai atlikti tyrimai rodo, kad vienas pagrindinių periodontito sukėlėjų Porphyromona gingivalis gali būti atsakingas už anticiklinio citrulinuoto peptido antigenų sintezę, kurie yra pagrindiniai reumatoidinio artrito markeriai. Bakterinės infekcijos ir reumatoidinio artrito jungiančioji grandis galėtų būti P. gingivalis išskiriamos peptidilarginino deaminazės. Tikėtina, kad PPAD, citrulinuodama žmogaus baltymus, galėtų suformuoti sisteminius autoantigenus ir paskatinti anti-CCP antikūnų atsiradimą. Be to, nauji tyrimai patvirtino PPAD autocitrulinaciją. PPAD kaip citrulinuotas bakterinis baltymas galėtų būti potencialus antigenas, kuris galėtų pažeisti šeimininko organizmo toleranciją citrulinuotiems baltymams ir dalyvauti RA patogenezėje. Išvados. Pastaruoju metu atliekama daug tyrimų norint nustatyti ryšį tarp periodontito ir reumatoidinio artrito, tačiau trūksta didesnių kontroliuojamų studijų šiuo klausimu, todėl vienareikšmiškų išvadų pateikti negalima. Atliktos studijos įrodo, kad genetiniai veiksniai lemia organizmo atsaką į lėtines ligas per kompleksinius patogenezės kelius. Remdamiesi epidemiologiniais duomenimis gydytojai reumatologai ir bendrosios praktikos gydytojai turėtų nukreipti RA sergančius pacientus pas odontologą arba periodontologą ištirti periodonto būklę.
The Effect of Predialysis Fistula Attempt on Risk of All-Cause and Access-Related Death
Authors: Quinn Robert R. , Oliver Matthew J. , Devoe Daniel , Poinen Krishnan , Kabani Rameez , Kamar Fareed , Mysore Priyanka , Lewin Adriane M. , Hiremath Swapnil , MacRae Jennifer , James Matthew T. , Miller Lisa , Hemmelgarn Brenda R. , Moist Louise M. , Garg Amit X. , Chowdhury Tanvir T. , Ravani Pietro
Published: October 2016

Whether the lower risk of mortality associated with arteriovenous fistula use in hemodialysis patients is due to the avoidance of catheters or if healthier patients are simply more likely to have fistulas placed is unknown. To provide clarification, we determined the proportion of access-related deaths in a retrospective cohort study of patients aged ≥18 years who initiated hemodialysis between 2004 and 2012 at five Canadian dialysis programs. A total of 3168 patients initiated dialysis at the participating centers; 2300 met our inclusion criteria. Two investigators independently adjudicated cause of death using explicit criteria and determined whether a death was access-related. We observed significantly lower mortality in individuals who underwent a predialysis fistula attempt than in those without a predialysis fistula attempt in patients aged <65 years (hazard ratio [HR], 0.49; 95% confidence interval [95% CI], 0.29 to 0.82) and in the first 2 years of follow-up in those aged ≥65 years (HR0–24 months, 0.60; 95% CI, 0.43 to 0.84; HR24+ months, 1.83; 95% CI, 1.25 to 2.67). Sudden deaths that occurred out of hospital accounted for most of the deaths, followed by deaths due to cardiovascular disease and infectious complications. We found only 2.3% of deaths to be access-related. In conclusion, predialysis fistula attempt may associate with a lower risk of mortality. However, the excess mortality observed in patients treated with catheters does not appear to be due to direct, access-related complications but is likely the result of residual confounding, unmeasured comorbidity, or treatment selection bias.