Digital gestützte Biodiversitätsexkursionen

Digitally supported excursions focusing on biodiversity The current study was conceived in order to constructively counteract the lack of essential experiences of nature and biodiversity knowledge of students. It combines the three fields “biodiversity”, “education” and “biology instruction“ outside the classroom in a context of environmental education in the Thuringian nature reserve Schiefergebirge/Obere Saale with regard to education as a necessary condition for any planned protection of biodiversity worldwide. The pedagogical proceeding focusing the concept of biodiversity was developed for biology instruction outside the classroom by integrating digital media into the learning process in a constructive way. On the basis of a ten-step procedure, biologically based GPS tours (“biotracks”) were created and tested in practice. For this purpose, two student excursions were designed: the first for grade 7 students in the vicinity of Heberndorf, the second for grade 9 students in the Bleilochstausee region. The results of the knowledge tests and records of the excursion journals from both groups indicate positive effects on studentś biodiversity knowledge. The pre-post questionnaires of the grade 7 students reveal the positive effects of biotracks on studentś attitudes and intentional behavior with respect to biodiversity.     

Brain wiring with composite instructions

The quest for molecular mechanisms that guide axons or specify synaptic contacts has largely focused on molecules that intuitively relate to the idea of an “instruction.” By contrast, “permissive” factors are traditionally considered background machinery without contribution to the information content of a molecularly executed instruction. In this essay, I recast this dichotomy as a continuum from permissive to instructive actions of single factors that provide relative contributions to a necessarily collaborative effort. Individual molecules or other factors do not constitute absolute instructions by themselves; they provide necessary context for each other, thereby creating a composite that defines the overall instruction. The idea of composite instructions leads to two main conclusions: first, a composite of many seemingly permissive factors can define a specific instruction even in the absence of a single dominant contributor; second, individual factors are not necessarily related intuitively to the overall instruction or phenotypic outcome.     

Parrots and Poets in Late Medieval Literature

ABSTRACT

Parrots have been kept as pets in the West since Classical antiquity, and they appear frequently in art. However, they are rarely represented in European literature until the end of the Middle Ages. “Le Chevalier du Papegau” (late fourteenth century, anonymous), “Les Epîtres de l'Amant Vert” (1505) by Jean Lemaire de Belges, and “The Testament and Complaynt of Our Soverane Lordis Papyngo” (1529) by Sir David Lindsay all employ speaking parrot protagonists. Analysis and comparison of the parrot characters in these three works demonstrates some of the ways in which the parrot species' ability to mimic human speech provides a vehicle which medieval and Renaissance authors used for entertainment, social commentary, and moral instruction.     

Movement of tropomyosin during regulation of vertebrate skeletal muscle: a simple physical model.

Using data obtained from (a) X-ray diffraction patterns of vertebrate skeletal muscle (b) three dimensional reconstructions from electron micrographs of in vitro aggregates of the thin filament proteins in the switched “on” and “off” positions (c) the analysis of the sequence of tropomyosin, a simple model can be proposed which may explain the geometrical arrangement of actin, tropomyosin and troponin during regulation. The “cooperative” behaviour exhibited by the thin filament can also be explained in terms of this arrangement.     

Secondary structural and “active site” momologies between nerve growth factor and insulin

Secondary structural elements, α-helix, β-sheet and turns, of nerve growth factor (NGF) were predicted by the method of Chou and Fasman. Analysis of the prediction results showed the presence of domain structure in NGF; the second half of the polypeptide chain showed a secondary structural “pattern” very similar to the first half. Comparison of the secondary structure of NGF and proinsulin showed significant homology between the B-chain, which has the “active site”, and NGF^25–54 The homology is reinforced by the identification of a pentapeptide sequence in NGF which is very similar to the “active site” sequence of insluin essential for receptor binding and agonist activity. The present alignment of insulin and NGF is however different from that proposed earlier on the basis of sequence data alone.     

Evolutionary relationships and sequence-structure determinants in human SARS coronavirus-2 spike proteins for host receptor recognition

Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of SARS CoV and SARS CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection in humans. Our results show that among the genomes analyzed, two sequence regions in the N-terminal domain “MESEFR” and “SYLTPG” are specific to human SARS CoV-2. In the receptor-binding domain, two sequence regions “VGGNY“ and ”EIYQAGSTPCNGV” and a disulfide bridge connecting 480C and 488C in the extended loop are structural determinants for the recognition of human ACE-2 receptor. The complete genome analysis of representative SARS CoVs from bat, civet, human host sources, and human SARS CoV-2 identified the bat genome (GenBank code: MN996532.1) as closest to the recent novel human SARS CoV-2 genomes. The bat SARS CoV genomes (GenBank codes: MG772933 and MG772934) are evolutionary intermediates in the mutagenesis progression toward becoming human SARS CoV-2.     

Lessons from EEO: Toward a Universal Evolutionary Curriculum

We propose a human-centered evolutionary curriculum based around the three questions: Who am I? Where do I come from? How do I fit in? We base our curriculum on our experiences as an evolutionary biologist/paleontologist (NE) and as a secondary level special education science teacher (GE)—and not least from our joint experience as co-editors-in-chief of this journal. Our proposed curriculum starts and ends with human biology and evolution, linking these themes with topics as diverse as the “tree of life” (systematics), anthropology, Charles Darwin, cultural evolution, ecology, developmental biology, molecular evolution/genetics, paleontology, and plate tectonics. The curriculum is “universal” as it is designed to be taught at all levels, K–16. The curriculum is flexible: “modules” may be expanded and contracted, reordered, or modified to fit specific grade level needs—and the requirements and interests of local curricula and teachers. We further propose that students utilize workbooks from online or printed sources to investigate the local answers to the general questions (e.g., “Who am I?”), while classroom instruction is focused on the larger scale issues outlined in the modules of our curriculum.     

Structures of Arg‐ and Gln‐type bacterial cysteine dioxygenase homologs

In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ～15–30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are some that conserve an active site Arg residue (“Arg‐type” enzymes) and some having a Gln substituted for this Arg (“Gln‐type” enzymes). Here, we describe a structure from each of these enzyme types by analyzing structures originally solved by structural genomics groups but not published: a Bacillus subtilis “Arg‐type” enzyme that has cysteine dioxygenase activity (BsCDO), and a Ralstonia eutropha “Gln‐type” CDO homolog of uncharacterized activity (ReCDOhom). The BsCDO active site is well conserved with mammalian CDO, and a cysteine complex captured in the active site confirms that the cysteine binding mode is also similar. The ReCDOhom structure reveals a new active site Arg residue that is hydrogen bonding to an iron‐bound diatomic molecule we have interpreted as dioxygen. Notably, the Arg position is not compatible with the mode of Cys binding seen in both rat CDO and BsCDO. As sequence alignments show that this newly discovered active site Arg is well conserved among “Gln‐type” CDO enzymes, we conclude that the “Gln‐type” CDO homologs are not authentic CDOs but will have substrate specificity more similar to 3‐mercaptopropionate dioxygenases.     

Evidence concerning the morphogenesis of saccular receptors in the bullfrog (Rana catesbeiana)

A dichotomy of hair-cell types has been found in the bullfrog sacculus, and considerable evidence supports the view that one type (“peripheral”) is transformed during macular growth to the other type (“central”). Between the periphery and the center of the macula, one finds a gradation of form from “peripheral” to “central” type. Occasionally in adults and more often in stage-26 tadpoles one finds the presumably younger peripheral type of hair cell occurring well beyond the limits of the macula proper. The apparent morphogenic sequence for saccular hair cells is (1) development of a kinocillum on an endolymphatic epithelial cell, (2) gradual transformation of microvilli into stereocilia, (3) growth of the stereocilia and development of kinociliary bulb, (4) achievement of final size and form.     

Molecular characterization of phytoplasma diseases of pepper in Turkey

During autumn, an extensive survey was conducted in pepper (Capsicum annum L.) in intensive cultivation areas of four provinces in southeastern Turkey (Adana, Kahramanmara?, Mersin and ?anl?urfa) in order to identify the causal agent (s) of phytoplasma‐like symptoms (chlorosis, little‐leaf, short internodes and stunting). DNA amplification by PCR and RFLP analysis using EcoRI restriction enzyme confirmed the presence of phytoplasmas in ?anl?urfa and Mersin, and consequently their possible association with the symptoms. Sequencing and phylogenetic analysis revealed that the isolate from ?anl?urfa had 99% sequence identity with “Candidatus Phytoplasma trifolii” (16SrVI) and is a member of the clover proliferation group (16SrVI‐A). Additionally, the isolate from Mersin had 96% sequence identity with “Candidatus Phytoplasma asteris” (16SrI). Importantly, gene sequence of the Mersin isolate shared <97.5% similarity to previously discovered “Ca. Phytoplasma” species. Consequently, the phytoplasma detected from Mersin could represent a new “Ca. Phytoplasma” species and to our knowledge, this is the first report of asteris‐like phytoplasmas infecting pepper in Turkey.     

Molecular Markers of Ph1 Gene in Chinese Spring and Development of Winter Wheat New Line Harboring ph1b Gene

he genomic DNA of common wheat (Triticum aestivum L.) “Chinese Spring” (CS) and its ph1b mutant were analyzed by using 19 sequence tagged site PCR (STS-PCR) primers, which derived from RFLP probes from barley (Hordeum vulgare L.) chromosome 5H. One marker was identified on wheat chromosome 5BL, which is 5.7 cM (centiMorgan) proximal to Ph1 gene, using the CS homoeologous group 5 nullisomic-tetrasomic, ditelosomic 5BL line and an F2 population from CS×ph1b mutant. This linked PCR marker was converted into a more specific sequence characterized amplified region (SCAR) marker. To obtain a new winter wheat line containing ph1b gene, the authors used a nullisomic 5B line of “Abbodanza”as a bridge parent and crossed respectively with the CS ph1b mutant (donor) and a winter wheat variety, “Jing 411” (recipient). The meiotic chromosome pairing was checked in the progeny of each cross, as well as using the marker-assistant selection of the SCAR marker identified for ph1b gene. After three inter-crossing and one selfing, a relatively stable ph1b substitution line of winter wheat with “Jing 411” background was obtained.     

Conformational dynamics of a short antigenic peptide in its free and antibody bound forms gives insight into the role of β‐turns in peptide immunogenicity

Earlier immunological experiments with a synthetic 36‐residue peptide (75‐110) from Influenza hemagglutinin have been shown to elicit anti‐peptide antibodies (Ab) which could cross‐react with the parent protein. In this article, we have studied the conformational features of a short antigenic (Ag) peptide (⁹⁸YPYDVPDYASLRS¹¹⁰) from Influenza hemagglutinin in its free and antibody (Ab) bound forms with molecular dynamics simulations using GROMACS package and OPLS‐AA/L all‐atom force field at two different temperatures (293 K and 310 K). Multiple simulations for the free Ag peptide show sampling of ordered conformations and suggest different conformational preferences of the peptide at the two temperatures. The free Ag samples a conformation crucial for Ab binding (β‐turn formed by “DYAS” sequence) with greater preference at 310 K while, it samples a native‐like conformation with relatively greater propensity at 293 K. The sequence “DYAS” samples β‐turn conformation with greater propensity at 310 K as part of the hemagglutinin protein also. The bound Ag too samples the β‐turn involving “DYAS” sequence and in addition it also samples a β‐turn formed by the sequence “YPYD” at its N‐terminus, which seems to be induced upon binding to the Ab. Further, the bound Ag displays conformational flexibility at both 293 K and 310 K, particularly at terminal residues. The implications of these results for peptide immunogenicity and Ag–Ab recognition are discussed. Proteins 2015; 83:1352–1367. © 2015 Wiley Periodicals, Inc.     

高职高专医学遗传学"三联系"教学模式初探

摘要: 根据高职高专教育规律、培养目标, 结合高职高专学制、课时及学生特点, 建立了以遗传病为主线的“教学内容与培养目标相联系, 理论教学与临床应用相联系, 实践教学与职业能力相联系”的“三联系”教学模式。三年的教改实践证明: 此种教学模式定位比较合理, 有助于激发学生的学习兴趣, 提高医学遗传学的综合 成绩。     

Genotype-phenotype mapping with polyominos made from DNA origami tiles

The correlation between genetic information and characteristics of a living cell—its genotype and its phenotype—constitutes the basis of genetics. Here, we experimentally realize a primitive form of genotype-phenotype mapping with DNA origami. The DNA origami can polymerize into two-dimensional lattices (phenotype) via blunt-end stacking facilitated by edge staples at the seam of the planar DNA origami. There are 80 binding positions for edge staples, which allow us to translate an 80-bit long binary code (genotype) onto the DNA origami. The presence of an edge staple thus corresponds to a “1” and its absence to a “0.” The interactions of our DNA-based system can be reproduced by a polyomino model. Polyomino growth simulations qualitatively reproduce our experimental results. We show that not only the absolute number of base stacks but also their sequence position determine the cluster size and correlation length of the orientation of single DNA origami within the cluster. Importantly, the mutation of a few bits can result in major morphology changes of the DNA origami cluster, while more often, major sequence changes have no impact. Our experimental realization of a correlation between binary information (“genotype”) and cluster morphology (“phenotype”) thus reproduces key properties of genotype-phenotype maps known from living systems.     

Sequence Analysis and Comparative Bioinformatics Study of Camelysin Gene (<Emphasis Type="Italic">calY</Emphasis>) Isolated from <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis>

Bacillus strains have been widely used for the production of fibrinolytic enzymes having role in the treatment of cardiovascular disorders. Purification and overproduction of such enzymes has increased their usage in medical fields including metalloproteinases with the ability to degrade extracellular matrix (ECM). Camelysin, a neutral metalloproteinase has been isolated from different species of bacteria like Bacillus cereus, Bacillus anthracis, and Bacillus thuringiensis with fibrinolytic, collagenolytic and actin degradation activity. This project successfully demonstrated the presence of 734-bp coding DNA sequence (CDS) encoding a 20.72331 kDa camelysin gene in local strain of Bacillus thuringiensis containing a signal peptide with cleavage site between residues 19 and 20. The sequence was submitted to GenBank (KT023597) and the sequence showed high homology with the camelysin protein of closely related Bacillus species. The alignment of related proteins through ClustalW displayed difference of four amino acids (“Q” replaced by “P” at position 169 and at position 182–184, “NQE” replaced by “HLK”) in the isolated protein. Comparison including structural and functional analysis of camelysin sequences isolated from different Bacillus species was carried out using different bioinformatics tools and software. The information would help in better understanding the properties of camelysin protein and its role in pathogenicity and clinical treatments.     

Set-Related Activity in the Premotor Cortex of Rhesus Monkeys: Effect of Triggering Cues and Relatively Long Delay Intervals

“Set-related activity” has been defined as a significant alteration in neuronal discharge rate during an “instructed delay period,” a period when a previously instructed movement is being withheld. It has been argued that set-related activity in the primate premotor cortex, or at least a significant proportion of it, reflects motor preparation. In most previous investigations, however, in which visual stimuli have triggered the movement and simultaneously indicated its target, set-related activity might reflect either the anticipation of or attention to the trigger stimulus. The present report shows that set-related activity is robust and can be directionally selective when trigger stimuli do not indicate the target and when a trigger stimulus is absent. Another feature of previous studies has been the relatively brief intervals between the instruction and trigger stimuli (typically 3 sec or less). In the present study, we were able to observe the activity of a small number of cells during longer delay periods. Set-related activity persists, although it becomes less consistent, for as much as 7.5 sec after an instruction stimulus. These results support the hypothesis that set-related activity reflects the preparation for specific limb movements.