Analysis of pir gene expression across the Plasmodium life cycle

Background Plasmodium interspersed repeat (pir) is the largest multigene family in the genomes of most Plasmodium species. A variety of functions for the PIR proteins which they encode have been proposed, including antigenic variation, immune evasion, sequestration and rosetting. However, direct evidence for these is lacking. The repetitive nature of the family has made it difficult to determine function experimentally. However, there has been some success in using gene expression studies to suggest roles for some members in virulence and chronic infection. Methods Here pir gene expression was examined across the life cycle of Plasmodium berghei using publicly available RNAseq data-sets, and at high resolution in the intraerythrocytic development cycle using new data from Plasmodium chabaudi. Results Expression of pir genes is greatest in stages of the parasite which invade and reside in red blood cells. The marked exception is that liver merozoites and male gametocytes produce a very large number of pir gene transcripts, notably compared to female gametocytes, which produce relatively few. Within the asexual blood stages different subfamilies peak at different times, suggesting further functional distinctions. Representing a subfamily of its own, the highly conserved ancestral pir gene warrants further investigation due to its potential tractability for functional investigation. It is highly transcribed in multiple life cycle stages and across most studied Plasmodium species and thus is likely to play an important role in parasite biology. Conclusions The identification of distinct expression patterns for different pir genes and subfamilies is likely to provide a basis for the design of future experiments to uncover their function.

Analysis of Pir Gene Expression Across the Plasmodium Life Cycle

Background Plasmodium interspersed repeat ( pir ) is the largest multigene family in the genomes of most Plasmodium species. A variety of functions for the PIR proteins which they encode have been proposed, including antigenic variation, immune evasion, sequestration and rosetting. However, direct evidence for these is lacking. The repetitive nature of the family has made it difficult to determine function experimentally. However, there has been some success in using gene expression studies to suggest roles for some members in virulence and chronic infection. Methods Here we examined pir gene expression across the life cycle of P. berghei using publicly available RNAseq data-sets, and at high resolution in the intraerythrocytic development cycle using new data from P. chabaudi . Results Expression of pir genes is greatest in stages of the parasite which invade and reside in red blood cells. The marked exception is that liver merozoites and male gametocytes produce a very large number of pir gene transcripts, notably compared to female gametocytes, which produce relatively few. Within the asexual blood stages different subfamilies peak at different times, suggesting further functional distinctions. Representing a subfamily of its own, the highly conserved ancestral pir gene warrants further investigation due to its potential tractability for functional investigation. It is highly transcribed in multiple life cycle stages and across most studied Plasmodium species and thus is likely to play an important role in parasite biology. Conclusions By identifying distinct expression patterns for different pir genes and subfamilies we hope to provide a basis for the design of future experiments to uncover their function.

Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness

Individual cell shape and integrity must precisely be orchestrated during morphogenesis. Here, we determine function of type II cadherins, Cdh6, Cdh8, and Cdh11, whose expression combinatorially demarcates the mouse neural plate/tube. While CRISPR/Cas9-based single type II cadherin mutants show no obvious phenotype, Cdh6/8 double knockout (DKO) mice develop intermingled forebrain/midbrain compartments as these two cadherins’ expression opposes at the nascent boundary. Cdh6/8/11 triple, Cdh6/8 or Cdh8/11 DKO mice further cause exencephaly just within the cranial region where mutated cadherins’ expression merges. In the Cdh8/11 DKO midbrain, we observe less-constricted apical actin meshwork, ventrally-directed spreading, and occasional hyperproliferation among dorsal neuroepithelial cells as origins for exencephaly. These results provide rigid evidence that, by conferring distinct adhesive codes to each cell, redundant type II cadherins serve essential and shared roles in compartmentalization and neurulation, both of which proceed under the robust control of the number, positioning, constriction, and fluidity of neuroepithelial cells.

Calcified gill filaments increase respiratory function in fishes

The morphology of fish gills is closely linked to aerobic capacity and tolerance of environmental stressors such as hypoxia. The importance of gill surface area is well studied, but little is known about how the mechanical properties of gill tissues determine function. In some fishes, the bases of the gill filaments are surrounded by a calcified ‘sheath' of unknown function. We tested two non-exclusive hypotheses: (i) calcified gill filaments enhance water flow through the gill basket, improving aquatic respiratory function, and (ii) in amphibious fishes, calcification provides support for gills out of water. In a survey of more than 100 species of killifishes and related orders, we found filament calcification was widespread and thus probably arose before the evolution of amphibious lifestyles in killifishes. Calcification also did not differ between amphibious and fully aquatic species, but terrestrial acclimation caused calcium deposition on the filaments of the killifish Kryptolebias marmoratus , suggesting a possible structural role when out of water. We found strong evidence supporting a role for filament calcification in enhancing aquatic respiratory function. First, acclimation to increased respiratory demands (hypoxia, elevated temperatures) induced calcium deposition on the filaments of K. marmoratus . Next, gentle removal of filament calcification decreased branchial resistance to water flow, indicating disruption of gill basket positioning. Thus, the mechanical properties of the gill filaments appear to play an important and previously unappreciated role in determining fish respiratory function.

Chromatin features define adaptive genomic regions in a fungal plant pathogen

ABSTRACTUnderstanding the complex information stored in a genome remains challenging since multiple connected regulatory mechanisms act at various scales to determine function. Increased comprehension of genome function at scales beyond contiguous nucleotides will help understand genetic diseases, the emergence of pathogenesis, and more broadly the genomics of adaptation. Here we report the analysis of DNA methylation, histone modification, and DNA accessibility in the plant pathogenic vascular wilt fungus Verticillium dahliae. Functional analysis details that DNA methylation is restricted to repetitive elements, such as transposable element DNA, but interestingly only some repetitive DNA is methylated. This incomplete DNA methylation is associated with repetitive DNA residing in specific compartments of the genome that were previously defined as Lineage-Specific (LS) regions. These regions are hypervariable between V. dahliae isolates and contain genes that support host colonization and adaptive traits. LS regions are associated with H3 Lys-27 methylated histones (H3K27me3), and repetitive DNA within LS regions are more transcriptionally active and have increased DNA accessibility, representing a hybrid chromatin state when compared to repetitive regions within the core genome. We used machine learning algorithms trained on epigenetic and DNA accessibility data to predict LS regions with high recall, identifying approximately twice as much LS DNA in the V. dahliae genome as previously recognized. Collectively, these results characterize LS regions in an intermediate chromatin state and provide evidence that links chromatin features and genome architecture to adaptive regions within the genome.

An Examination of the Performance of Blank Cartridges Used in Captive Bolt Devices for the Pre-Slaughter Stunning and Euthanasia of Animals

Blank cartridges provide the power source for the majority of captive bolt devices used for rendering animals unconscious prior to slaughter within the United Kingdom or euthanasia worldwide. This paper presents the results of the examination of cartridges as one of the variables that can contribute to an unsuccessful application of this method in practice. Variation was found in cartridge weight, propellant fill volume and velocity within boxes of 1000 cartridges. The variation found was greater in lower charge (1.00 grain) cartridges than in 3.00 grain cartridges, however velocity was found to be variable in both sets. For example, in vivo velocity measurements with 0.25″ calibre 3.00 grain cartridges demonstrated an average velocity of 50.8 m/s over 200 shots with a range of 35.7 to 62.9 m/s when used in the same device. This work demonstrates that variation in cartridge performance does occur and can be due to various factors such as fill volume and propellant function, and simply weighing cartridges cannot be used to determine function, therefore cartridge performance must be a factor that is considered in the event of a miss-stun.

FUNGSI DAN TEKNIK PERMAINAN ALAT MUSIK TRADISIONAL MANDAILING UYUP-UYUP DI DESA PARGARUTAN JAE TAPANULI SELATAN

This study aims to determine Function, Game Techniques and Organic Uyup-Uyup In PargarutanVillage Jae Tapanuli Selatan. The purpose of this research is to know the function, game techniqueand organology of mandailing uyup-uyup instrument in Pargarutan Jae Tapanuli Selatan Villagecommunity. The theory used is function, game technique and organology. The function of music isto express the taste and simultaneously as an activity of various types of human communication.Organology is the study of the structure of musical instruments based on sound sources, how toproduce sounds and system of alignment. Game technique is a way or technique of touch on amusical instrument over a particular tone according to the instructions or notation. The methodused in this research is qualitative descriptive method. The sample in this research is one artist andfive people of Pargarutan Jae Village. Data collection was done by observation, interview, anddocumentation. This research was taken in Pargarutan Jae Village, and this research was carriedout from October 2017. The function of Uyup-uyup music instrument in South Tapanuli there arethree of the first is the function of emotional disclosure is a medium for someone to express feelingsand emotional through the game of uyup-uyup instruments that use systematic way of presentingthe sound. The second is the entertainment function in which the South Tapanuli also needentertainment that is the entertainment of playing a uyup-uyup instrument at rest in the rice fields.Third is the Communication Function where when calling the opposite sex across the paddy fieldthe man repeatedly played uyup-uyup. Organic musical instrument Uyup-uyup consists of fiveparts, namely rice stalks, coconut leaves and lidi as a binder of coconut leaves. The game techniquein the uyup-uyup instrument is divided into the first three sections that are played in a sitting /standing position, the second way of blowing uyup-uyup is by way of the mouth is placed at thebase of the top of the uyup-uyup instrument, the third position of the finger finger, first startingfrom the left hand with the beginning of the index finger and the second hole of the middle fingerand then on the right hand begins with the index finger and the hole of both middle fingers.

Connecting Structure–Property and Structure–Function Relationships across the Disciplines of Chemistry and Biology: Exploring Student Perceptions

While many university students take science courses in multiple disciplines, little is known about how they perceive common concepts from different disciplinary perspectives. Structure–property and structure–function relationships have long been considered important explanatory concepts in the disciplines of chemistry and biology, respectively. Fourteen university students concurrently enrolled in introductory chemistry and biology courses were interviewed to explore their perceptions regarding 1) the meaning of structure, properties, and function; 2) the presentation of these concepts in their courses; and 3) how these concepts might be related. Findings suggest that the concepts of structure and properties were interpreted similarly between chemistry and biology, but students more closely associated the discussion of structure–property relationships with their chemistry courses and structure–function with biology. Despite receiving little in the way of instructional support, nine students proposed a coherent conceptual relationship, indicating that structure determines properties, which determine function. Furthermore, students described ways in which they connected and benefited from their understanding. Though many students are prepared to make these connections, we would encourage instructors to engage in cross-disciplinary conversations to understand the shared goals and disciplinary distinctions regarding these important concepts in an effort to better support students unable to construct these connections for themselves.

Survival Analysis of Child Patient Diarrhea Using Kaplan Meier Method and Rank Log Test

Diarrhea being one of public health problems that important because it is third major contributor the pain children in various countries including indonesia. This research using data from islam hospital medical record jakarta in january 2017 shows that diarrhea cases were occupying the highest rank of various types of disease in patients children, using indicators long healed patients , the age of , andsex. Methods used to determine function survival who dominated in patients children are Kaplan Meier and Log Rank. The results of the analysis method kaplan meier got that patients male had the probability of healed longer than for patients female as well as patients age of 6- 11 years had the probability healed longer than the age of ≤ 5 years. To Log Rank test got that there is no significant difference between the survival function based on sex and age patients.