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2.2: Illustrations - Biology

2.2: Illustrations - Biology



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Below, all black and white illustrations were provided by Georgij Vinogradov and Michail Boldumanu.


2.2: Illustrations - Biology

Submission Guidelines

1. Manuscript types

Original articles. There is no page limit, but 15-25 printed pages are the most usual. There is no figure limit, but they should be strictly necessaries. There is no limit for tables, but they should be strictly necessaries and easy to understand and reproduce in the published paper. Supplementary material should be restricted to extensive figures and tables not necessaries for the interpretation of the results, but that could give more information to readers interested in some particular procedure or method.

Reviews. Same comments that for original articles. They should be written by experienced authors with several published articles in the subject revised.

Invited reviews. Same comments than for original articles. It can be submitted after invitation of the editor of the Journal. They are free or charges.

2. Manuscript submission
Please make your submission online at https://www.editorialmanager.com/hh/default.aspx. The text document must be saved as Word or RTF format. Tables must be included in the text document. Figures must be saved in the formats and at the resolution below indicated.

2.1. Submission of a manuscript implies:
1) The work described has not been previously published, except in abstract form in a Congress
2) The work described is not under consideration for publication anywhere else
3) The publication of manuscript in Histology and Histopathology is approved by all co-authors
4) The publisher will not be held legally responsible should there be any claims for compensation
5) The authors should have obtained permission from the copyright owner for any figures or tables previously published. They should retain the permission documents and the previous publication should be properly cited. Any material received without such evidence will be assumed to originate from the authors.
6) Authors must maintain all the raw data. They could be asked by the Journal if necessary. If they are not suitable, the article could be retracted.

2.2. Manuscripts should have:
2.2.1) A concise cover letter.

2.2.2) A title page. Title page should contain the title, author list (given and family name, but not degree), affiliation, contact details for corresponding author, key words (different to those in the title) and short title.

2.2.3) An abstract. About 250 words.

2.2.4) Main text for original articles
Do not divide words at the end of lines. Pages should be numbered.
References to the literature should be cited in the text by the name of the author(s) followed by the year of publication. In cases in which there are more than two authors, only the first is named, followed by "et al.". Examples: Smith (1980) reported that. (Smith, 1980, 1982) (Smith and Tanaka, 1980) (Smith et al., 1980). Suffixes a, b, etc., should be used following the year to distinguish two or more papers by the same author(s) published in the same year example (Smith, 1981a). When two or more references are included in the same bracket, they must be quoted in the chronological order example (Smith, 1980 Bell et al., 1984).
Main text for original articles should contain the sections:
a) List of abbreviations (if any)
b) Introduction
c) Material and methods
d) Results
e) Discussion
f) Acknowledgements, including funding sources
g) A conflict of interest statement
h) The reference list should be in alphabetical order.
References to articles in periodical publications must include: Names and initials of all authors, year of publication, complete title of paper, name of journal (abbreviated in accordance with PubMed), number of volume, and first and last page numbers. Example: Morita T., Suzuki Y. and Churg J. (1973). Structure and development of the glomerular crescent. Am. J. Pathol. 72, 349-368.
Reference to books must include: Name and initials of authors, year of publication, full title, edition, editor, publisher, place of publication and page numbers. Example: Powell D. and Skrabanek P. (1981). Substance P. In: Gut Hormones. 2nd ed. Bloom S.R. and Polak J.M. (eds). Churchill Livingstone. Edimburgh. pp 396-401.
i) Tables. Numbered in arabic
j) Figure legends. Including experimental group, technique, meaning of arrows or letters in the figures, magnification in the form of scale bars and any other information that help to understand the figure.

2.2.5) Main text for reviews. Like original articles, except for the sections Introduction, Material and methods, Results and discussion that are not mandatory. The authors are free to select different sections.

2.2.6) As separate files. Illustrations should not exceed 17.8 x 22.2 cm. The Editor reserves the right to reduce or enlarge the illustrations. Apply figure numbers to the lower left-hand corner of each photograph and the scale bar at the lower right-hand corner. Images should be TIFF file format, preferentially, although other formats could be useful (jpg, ppt, etc). Black and white figures must be at gray scale. Color figures should be preferentially in CMYK, but RGB is also allowed. Line art files must have a 500dpi resolution, while other images must have a 300dpi resolution.

3. Article processing charges (APCs)
The articles are published under a Creative Commons (CC BY) license. The price is 1,600.00 euros (tax excluded) independently of the number of color figures and pages.

4. Copyright and license term
The copyright remains with the author. author(s) agree to publish the article under the Creative Commons Attribution License CC BY

5. Review process
An initial assessment will be made by the Editor-in-Chief following submission of your manuscript. This process considers whether the submitted work falls within the scope of the Journal and is of initial interest and/or scientific worth to merit possible publication. Manuscripts that enter the review process may be assigned to the Editor-in-Chief, another Editor or a member of the Editorial Board who invites reviewers (normally two-three external reviews are sought). The reviewers&rsquo evaluations and Associate Editor&rsquos comments are submitted to the Editor-in-Chief (or the relevant Regional Editor) to inform a final decision. We aim to convey a decision within four weeks of the receipt of the manuscript. The review process is simple-blind type.
The Editor-in-Chief based on the reviewers&rsquo evaluations and with possibly with the help of a member of the Editorial Board will advise authors whether a manuscript is accepted, requires revision, or is rejected. Revisions are expected to be returned within a fixed time, depending on the extension of the modification suggested by the reviewers. Manuscripts not revised within this time are subject to withdrawal from consideration for publication unless there are extenuating circumstances. Please note that some manuscripts will have to be rejected on the grounds of priority, interest, journal balance and available space. Invitation to submit a revised manuscript does not imply that acceptance will automatically follow. The decision of the Editor-in-Chief is final. If, however, authors dispute a decision and can document good reasons why a manuscript should be reconsidered, a rebuttal process exists. In the first place, authors should write to the Editor-in-Chief outlining their case.

6. Post-acceptance procedures
Accepted Articles.Accepted Preprints version (authors' manuscripts of accepted articles, prior to copyediting, page layout and proofing) are available shortly after the day of acceptance for publication in our web site and in some indexing sites.
Proofs. Proofs in PDF format will be sent to the corresponding author for checking. This stage is to be used only to correct errors that may have been introduced during the production process. Prompt return of the corrected proofs, preferably within three days of receipt, will minimize the risk of the paper being held over to a later issue.


What the Human Machine Can Do

Imagine a machine that has all of the following attributes:

  • It can generate a “wind” of 166 km/hr (100 mi/hr).
  • It can relay messages faster than 400 km/hr (249 mi/hr).
  • It contains a pump that moves about a million barrels of fluid over its lifetime.
  • It has a control center that contains billions of individual components.
  • It can repair itself, if necessary.
  • It may not wear out for up to a century or more.

This machine has all of these abilities, and yet it consists mainly of water. What is it? It is the human body.


Entry of coronaviruses

Coronavirus S proteins are homotrimeric class I fusion glycoproteins that are divided into two functionally distinct parts (S1 and S2) (Fig. 2). The surface-exposed S1 contains the receptor-binding domain (RBD) that specifically engages the host cell receptor, thereby determining virus cell tropism and pathogenicity. The transmembrane S2 domain contains heptad repeat regions and the fusion peptide, which mediate the fusion of viral and cellular membranes upon extensive conformational rearrangements 10,11,12 . Shortly after the 2002–2003 SARS-CoV outbreak, ACE2 was identified as the functional receptor that enables infection by SARS-CoV 13 . The high genomic and structural homology between the S proteins of SARS-CoV and SARS-CoV-2 (76% amino acid identity) supported the identification of ACE2 as the cell-surface receptor for SARS-CoV-2 (refs 12,14,15,16 ). Remarkably, essential SARS-CoV contact residues that interact with ACE2 were highly conserved in SARS-CoV-2 as well as in members of the species Severe acute respiratory syndrome-related coronavirus that use ACE2 or have similar amino acid side chain properties 14,15,17,18,19 . These data were corroborated by the atomic resolution of the interface between the SARS-CoV-2 S protein and ACE2 (refs 16,19,20,21 ). By contrast, the bat Severe acute respiratory syndrome-related coronavirus RaTG13 S sequence (93.1% nucleotide identity to SARS-CoV-2) shows conservation of only one out of six amino acids directly involved in ACE2 binding, even though, based on the entire genomic sequence, RaTG13 is the closest relative of SARS-CoV-2 known to date (96.2%) 14 (Box 2).

a | Schematic illustration of coronavirus spike, indicating domain 1 and domain 2. The receptor-binding motif (RBM) is located on S1 and the fusion peptide (FP), heptad repeat 1 (HR1), HR2 and the transmembrane (TM) domains are located on S2. The cleavage sites are indicated. The colour code designates conserved spike regions surrounding the angiotensin-converting enzyme 2 (ACE2)-binding domain among severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs) and high amino acid sequence variations within the site of receptor interaction. b | Amino acid alignment of human SARS-CoV-2 (Wuhan-Hu-1) and SARS-CoV (Frankfurt-1), bat (RaTG13, RmYN02, CoVZC45 and CoVZXC21) and pangolin (MP789, P1E) SARSr-CoVs. The spike gene sequence alignment was performed using MUSCLE and using the default settings and codon alignment, then translated into amino acids using MEGA7, version 7.0.26. The alignment was coloured according to percentage amino acid similarity with a Blosum 62 score matrix. The colour code designates conserved spike regions surrounding the ACE2-binding domain among SARSr-CoVs and high amino acid sequence variations within the site of receptor interaction. The insertion of a polybasic cleavage site (PRRAR, amino acids 681 to 685) in Wuhan-Hu-1 is indicated, and similar insertions are depicted in bat SARSr-CoV RmYN02. c | Within the spike sequence, the ACE2 receptor-binding motif (amino acids 437 to 509, black line) is depicted. The spike contact residues for ACE2 interaction are marked with asterisks.

These data suggest that, much like during the evolution of SARS-CoV, frequent recombination events between severe acute respiratory syndrome-related coronaviruses that coexist in bats probably favoured the emergence of SARS-CoV-2 (ref. 22 ). Indeed, predicted recombination breakpoints divide the S gene into three parts. The middle part of the S protein (amino acids 1,030–1,651, encompassing the RBD) is most similar to SARS-CoV and bat severe acute respiratory syndrome-related coronaviruses WIV1 and RsSHC014, all of which use human ACE2 as a cellular entry receptor 23 . However, the amino-terminal and carboxy-terminal parts of the SARS-CoV-2 S protein (amino acids 1–1,029 and 1,651–3,804, respectively) are more closely related to severe acute respiratory syndrome-related coronaviruses ZC45 and ZXC21. These observations highlight the importance of recombination as a general mechanism contributing to coronavirus diversity and might therefore drive the emergence of future pathogenic human coronaviruses from bat reservoirs. This emphasizes the need for surveillance to determine the breadth of diversity of severe acute respiratory syndrome-related coronaviruses, to evaluate how frequently recombination events take place in the field and to understand which virus variants have the potential to infect humans. Increased surveillance is thus instrumental to improve our preparedness for future outbreaks of severe acute respiratory syndrome-related coronaviruses.

Besides receptor binding, the proteolytic cleavage of coronavirus S proteins by host cell-derived proteases is essential to permit fusion 24,25 . SARS-CoV has been shown to use the cell-surface serine protease TMPRSS2 for priming and entry, although the endosomal cysteine proteases cathepsin B (CatB) and CatL can also assist in this process 24,25,26,27,28 . Concordantly, the simultaneous inhibition of TMPRSS2, CatB and CatL efficiently prevents SARS-CoV entry into in vitro cell cultures 29 . TMPRSS2 is expressed in the human respiratory tract and thus strongly contributes to both SARS-CoV spread and pathogenesis. Notably, SARS-CoV-2 entry relies mainly on TMPRSS2 rather than on CatB and CatL, as inhibition of TMPRSS2 was sufficient to prevent SARS-CoV-2 entry in lung cell lines and primary lung cells 15,30 . These data support the evaluation of the TMPRSS2 inhibitors camostat mesylate and nafamostat mesylate in clinical trials, since in vitro studies have demonstrated their potent antiviral activity against emerging coronaviruses, including SARS-CoV-2 (refs 29,31,32 ).

Given these similarities in receptor usage and cleavage requirements, it is surprising that SARS-CoV and SARS-CoV-2 display marked differences in virus replication efficiency and spread. SARS-CoV primarily targets pneumocytes and lung macrophages in lower respiratory tract tissues, where ACE2 is predominantly expressed, consistent with the lower respiratory tract disease resulting from SARS-CoV infection and the limited viral spread 33,34,35 . By contrast, SARS-CoV-2 replicates abundantly in upper respiratory epithelia, where ACE2 is also expressed, and is efficiently transmitted 36,37,38 .

Different host cell tropism, replication kinetics and transmission of SARS-CoV and SARS-CoV-2 might be determined by S protein–ACE2 binding affinities. For example, it has been reported that the S protein and ACE2 binding affinity is correlated with disease severity in SARS-CoV infections 18 . The affinity of the SARS-CoV-2 RBD to ACE2 has been shown to be similar 16,19 or stronger 20,30 than that of the SARS-CoV RBD. However, the binding affinity of the entire SARS-CoV-2 S protein to ACE2 seems to be equal or lower than that of SARS-CoV, suggestive of a less exposed RBD 16,28,30 . In addition to ACE2, attachment and entry factors, such as cellular glycans and integrins or neuropilin 1, may also have an impact on the observed phenotypic differences of SARS-CoV and SARS-CoV-2 (refs 39,40,41,42,43 ).

A peculiar feature of the SARS-CoV-2 S protein is the acquisition of a polybasic cleavage site (PRRAR) at the S1–S2 boundary, which permits efficient cleavage by the prototype proprotein convertase furin. Cleavage results in enhanced infection and has been proposed to be a key event in SARS-CoV-2 evolution as efficient S protein cleavage is required for successful infection and is a main determinant in overcoming species barriers 10,11,12,15,16,28,30,44,45,46 . This pre-processing of the SARS-CoV-2 S protein by furin may contribute to the expanded cell tropism and zoonotic potential and might increase transmissibility 16,46 . Importantly, such cleavage sites have not been identified in other members of the Sarbecovirus genus 46 . However, there are multiple instances of furin-like cleavage site acquisitions that occurred independently during coronavirus evolution and similar cleavage sites are present in other human coronaviruses such as HCoV-HKU1 (ref. 47 ), HCoV-OC43 (ref. 48 ) and MERS-CoV 49 . Recently, an independent insertion of amino acids (PAA) at the same region of the S protein has been identified in the bat coronavirus RmYN02 (ref. 50 ). Such independent insertion events highlight the zoonotic potential of bat severe acute respiratory syndrome-related coronaviruses and may increase the possibility of future outbreaks.

The importance of coronavirus S protein-mediated receptor binding and temporally coordinated conformational rearrangements that result in membrane fusion make this process a prime target of innate and adaptive antiviral responses. Notably, a screen involving several hundred interferon-stimulated genes identified lymphocyte antigen 6 family member E (Ly6E) as a potent inhibitor of coronavirus fusion 51 . Ly6E-mediated inhibition of coronavirus entry was demonstrated for various coronaviruses, including SARS-CoV-2, and seems to have pivotal importance in protecting the haematopoietic immune cell compartment in a mouse model of coronavirus infection. Moreover, the exposure of S protein on the surface of the virion results in the induction of specific neutralizing humoral immune responses 52 . Coronavirus S proteins are heavily glycosylated, which promotes immune evasion by shielding epitopes from neutralizing antibodies 16,53,54 . Nevertheless, sera from patients with SARS and COVID-19 can neutralize SARS-CoV and SARS-CoV-2, respectively 15,28 . Several specific or cross-reactive antibodies that bind the SARS-CoV-2 S protein have been recently reported and their administration to infected patients could potentially provide immediate protection 55,56,57,58 . Human monoclonal antibodies from previous hybridoma collections from SARS-CoV S protein-immunized transgenic mice 55 or from the memory B cell repertoire of convalescent patients with SARS and COVID-19 have been shown to either directly interfere with RBD–ACE2 interaction 55,57,58,59 or to destabilize intermediate pre-fusion conformations upon binding different epitopes 55,56 . Taken together, the exploitation of a combination of multiple neutralizing antibodies that do not compete for overlapping epitopes may not only result in synergistic improvements but also impede the appearance of escape mutations.

Box 2 Diversity of severe acute respiratory syndrome-related coronaviruses

SARS-CoV-2 belongs to the species Severe acute respiratory syndrome-related coronavirus in the subgenus Sarbecovirus 1,14,23 . Phylogenetic relationships of representative members of the species Severe acute respiratory syndrome-related coronavirus were analysed (sequences retrieved from GenBank and GISAID were analysed using MEGA7 version 7.0.26, asterisks indicate representative viruses further depicted in figure part b). Interestingly, SARS-CoV-2 shared 79.6% nucleotide identity with SARS-CoV and close relations to severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs) ZC45 and ZXC21 from Rhinolophus sinicus, whereas RaTG13 from Rhinolophus affinis showed the highest nucleotide similarity of 96.2% 14,23 (figure part a).

Sequence identity differed highly upon comparison of individual genes and domains, indicating frequent recombination events in natural reservoir hosts 14,23,196 . This is exemplified by comparing the nucleotide identity of SARS-CoV-2 with bat coronavirus RaTG13, bat CoV RmYN02, pangolin CoV MP789, pangolin CoV P1E, bat CoV ZC45, bat CoV ZXC21 and human SARS-CoV (Frankfurt-1 strain). Remarkably, in all depicted SARSr-CoVs, the spike gene, a major determinant for zoonotic transmission to humans, showed lower sequence similarity with SARS-CoV-2, thus raising the question of the SARS-CoV-2 origin. Despite the detection of a wide variety of similar bat CoVs in China, SARS-CoV-2 or an immediate precursor have not been found, leaving the role of bats in the emergence of SARS-CoV-2 elusive. Moreover, the environmental separation of bats and humans might favour the existence of an intermediate host, responsible for SARS-CoV-2 adaption and transmission into the human population, just like civet cats were suggested in the SARS-CoV outbreak 197 . The example of pangolin CoV MP789, which shared five essential amino acids for ACE2 binding in the S with SARS-CoV-2 highlights the existence of a variety of unidentified betacoronaviruses in wild-life animals and their roles as possible intermediate hosts 198 . Nevertheless, the number of identified bat SARSr-CoVs represents only a fraction of the existing diversity. The recent identification of bat SARSr-CoVs that can use human ACE2 as an entry receptor (CoV WIV1, CoV bRsSHC014) indicates a possibility of direct cross-species transmission from bats to humans 20,199,200 (figure part b).


American Museum of Natural History Releases Vintage Drawings of Seashells

The American Museum of Natural History has released a set of postcards you can buy when you visit them – The Seashell Collector. I thought the set looks quite brilliant, and it’s definitely worth sharing, along with some basic information

Seashells

The word seashell is often used to mean only the shell of a marine mollusk – bivalves, gastropodes, etc. Seashells are the exoskeletons of mollusks such as snails, clams, oysters and many others, produced from calcium carbonate and small amounts of protein (under 2 percent). This particular illustration is over 200 years old – it appeared Le conchyliologie, or Histoire naturelle des coquilles de mer… by Antoine-Joseph Dezallier d’ Argenville and published in 1780.

Nautilus

The Nautilus is a marine mollusk some species have been around since the early Triassic, 250 million years ago, making some of the most popular fossils. But they’re still doing fine to this day. What makes them extremely special is that they approximate the logarithmic spiral almost perfectly. This image, created by engraver G.W. Knorr, appeared in the 1757 book Vergnügen der Augen und des Gemüths… (Pleasure of the Eyes and the Mind, 1757-72).

The Great Scallop (Pecten maximus)

French naturalist Jean Charles Chenu published these drawings Illustrations conchyliologiques ou description et figures de toutes les coquilles, surprising the beauty and lovely colors of the great scallop. This edible saltwater clam, a marine bivalve mollusk in the family Pectinidae can be found at depths up to 800 meters in the Mediterranean sea and the Eastern Atlantic,

Clear Sundial Snail (Architectonica perspectiva)

The clear sundial snail is a a marine gastropod mollusk, known as the staircase shells or sundials due to the color of their shell. This sea snail is found in sandy waters across the Indo-Pacific and these drawings first appeared in L.C. Keiner’s 12-volume series Species general et iconographie des coquilles vivantes…, published from 1834 to 1880.

Queen Conch (Lobatus gigas)

This species is one of the largest molluscs native to the Atlantic, reaching up to 35.2 centimetres (13.9 in) in shell length and weighing up to 2.2 kg (5 pounds). They can also live up to 40 years. This illustration appeared in Chenu’s Illustrations conchyliologiques ou description et figures de toutes les coquilles.

Textile Cones (Conus textile)

As beautiful as these seashells are, they are also very dangerous. The textile cone hunts by spearing it’s prey with a harpoon that delivers a cocktail of neurotoxins that can be fatal even to humans. Scientists are actually working to make new drugs and painkillers from their neurotoxins.


Biology Professor Explains What “Biological Sex” Really Means, Starts A Heated Debate On Twitter

Sad to say, prejudice, discrimination and bigotry are still a thing in many societies, and part of it stems from people&rsquos convictions regarding things like sex and gender identity.

In today&rsquos case, it particularly ties in with how the term biological sex is thrown about to justify one&rsquos beliefs on what and how humans ought to be.

Well, this one biologist explained on Twitter what biological sex actually is, that it&rsquos not as clear-cut as some might believe it to be, and that it shouldn&rsquot be considered a basis for bigotry and discrimination.

Sex and gender identity debates often include people throwing about the &lsquobiological sex&rsquo term, which this biologist decided to explain in more detail

Rebecca R. Helm is an Assistant Professor of Biology at the University of North Carolina, who studies ecology and evolution of how animals change through time.

Some time ago, she went to Twitter to tackle the term biological sex. You see, some people make it seem like it&rsquos all very simple, but Helm breaks it down and shows just how simple it really is.

Biologist Rebecca Helm posted a tweet thread detailing how &lsquobiological sex&rsquo isn&rsquot as simple as some may think

Now, there are several ways of approaching this: on a chromosomal, hormonal, or even cellular level. But none of them would allow you to reach a simple explanation.

Sure, you can say there are the XX/XY chromosomes and the SRY gene that really matters to sex here. But there&rsquos also a chance where SRY can pop off the chromosome and your physical, chromosomal, and genetic sex might vary altogether because of this without you even knowing it.

Helm tackles all aspects of human biology, including chromosomes, genes, cells, and even hormones

And it&rsquos the same level of complexity with the hormonal and cellular definitions too. There are abnormalities whereby women could be able to generate more male hormones than males themselves, but they would otherwise still look very much feminine. Would that make them male?

Same goes with cells&mdashthere&rsquos this thing with cells having receptors that hear sex hormones, but sometimes they don&rsquot work. Does that make them stuck between two traditional genders as a non-binary?

As you might have guessed, the possibilities here are endless, where you can be a different sex on a genetic, chromosomal, hormonal, cellular, and even physical level. Yep, this is totally not complicated at all.

Helm concluded that hence biological gender shouldn&rsquot be a basis to discriminate and judge people: &ldquoBiology is complicated. Kindness and respect don&rsquot have to be.&rdquo

The twitter thread went viral, gaining over 55k likes and even being reposted elsewhere

The tweet thread went viral among several communities. While some found this thread interesting and insightful, others were still trying to counter it on Twitter with constructive and not so constructive feedback.

Regardless, the Twitter thread gained over 55,000 likes and 27,000 retweets, and even found itself on Imgur, where it was viewed by another 80,000 people.

What are your thoughts on this? Let us know in the comment section below!

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Background

High-throughput single-cell transcriptome studies have thrived in animal and human research in recent years [1,2,3,4,5]. However, despite successful single-cell characterization at a relatively low scale in maize developing germ cells [6] and rice mesophyll cells [7] using capillary-based approaches [8], only a handful of large-scale single-cell RNA studies using high-throughput platforms such as 10x Genomics or Drop-seq [9] have been published in plants [10], most of which profiled protoplasts generated from the root of Arabidopsis [11,12,13,14,15,16,17,18,19]. A major reason for this narrow focus of tissue type is that plant cells are naturally confined by cell walls, and protoplasting is required to release individual cells—a procedure that is thoroughly tested for Arabidopsis roots [20,21,22] but remains to be difficult or impractical in many other tissues or species. Moreover, generating protoplasts from all cells uniformly is challenging given the complexity of plant tissues, and the enzymatic digestion and subsequent cleanup process during protoplast isolation may trigger the stress response and influence the transcriptome. Therefore, a protoplasting-free method is urgently needed to broaden the application of large-scale single-cell analysis in plants.

We recently characterized full-length nascent RNAs in Arabidopsis and unexpectedly found a large number of polyadenylated mRNAs that are tightly associated with chromatin [23]. Since it is considerably easier and more widely applicable to perform nucleus isolation on various plant tissues than protoplasting, we set out to test if the polyadenylated RNAs in a single nucleus are sufficient to convey information on cell identity using the 10x Genomics high-throughput single-cell platform. Besides the standard Illumina short-read library which primarily captures abundance information, long-read sequencing has recently been incorporated into single-cell studies [24,25,26]. To access the large number of intron-containing RNAs in plant nuclei, we also constructed a Nanopore-based long-read library and developed a bioinformatic pipeline named “snuupy” (single nucleus utility in python) to characterize mRNA isoforms in each nucleus (Fig. 1a, Additional file 1: Fig. S1). Here, we applied the flsnRNA-seq to root and endosperm, respectively, and demonstrated that the long-read single-nucleus strategy would enable plant biologists to bypass protoplasting and study RNA isoforms derived from alternative splicing and alternative polyadenylation (APA) at the single-cell level and provides additional dimensions of transcriptome complexity that could potentially further improve clustering or characterization of different cell types.

Protoplasting-free large-scale single-nucleus RNA-seq reveals the diverse cell types in Arabidopsis root. a Schematic diagram of protoplasting-free single-nucleus RNA-seq. b Incompletely spliced and fully spliced fractions of the Nanopore reads from our single-nucleus RNA library, compared with a previously published total RNA library (Parker et al., eLife, 2020). c UMAP visualization of the various cell types clustered using Illumina single-nucleus data (upper panel), and cartoon illustration of major cell types in Arabidopsis root tip (lower panel). d Violin plots showing the expression levels of previously reported cell type-specific marker genes in 14 clusters


MATERIALS AND METHODS

Animals and animal preparation

Adult leeches (Hirudo verbana Carena 1820) were obtained from Niagara Leeches (Niagara Falls, NY, USA) and maintained under standard conditions (Harley et al., 2011). At the time of the experiments, leeches had fasted for at least 2 months and weighed 1–1.5 g. Leeches were anesthetized with ice-cold leech saline (Tomina and Wagenaar, 2018) and immobilized ventral-side up on dark silicone (Sylgard 170, Dow Corning, Midland, MI, USA) using insect pins stuck in annuli without sensilla. The head of the leech was pinned against the dark silicone so that the eye cups faced the silicone and thus would not directly receive stimulation light. The body wall was opened from midbody segments M8 to M11 (or M7 to M10 in experiments on spectral sensitivity under full dark adaptation). The lateral roots of ganglia M9 and M10 (or M8 and M9) were transected, and the ganglia and connectives were gently separated from the body tissue without severing any other nerves. The wall of the ventral blood sinus (‘stocking’) was removed between the exposed ganglia. A thin strip of silicone (Sylgard 184) was slipped between the nerve cord and the body wall and pinned down on each side of the leech. Ganglia M9 and M10 (or M8 and M9) were pinned very close together onto the silicone strip and the connective between them was sucked into a suction electrode. The general setup is shown in Fig. 1A. The temperature of the leech was kept at 15–19°C throughout all experiments.

Experimental setup. (A) Illustration of how leeches were pinned out, with a silicone bridge slipped underneath the nerve cord, the ventral body wall opening that was made between M8 and M11, and the suction electrode. (B) Orientation of the background and stimulus LED light sources relative to the leech for all experiments that tested the adaptation to background light illumination (Figs 3 and 4). (C) Orientation and placement of the LED light source and the barrier between the anterior and posterior side for the experiments on non-local adaptation (Fig. 6) and spatial integration (Fig. 7).

Experimental setup. (A) Illustration of how leeches were pinned out, with a silicone bridge slipped underneath the nerve cord, the ventral body wall opening that was made between M8 and M11, and the suction electrode. (B) Orientation of the background and stimulus LED light sources relative to the leech for all experiments that tested the adaptation to background light illumination (Figs 3 and 4). (C) Orientation and placement of the LED light source and the barrier between the anterior and posterior side for the experiments on non-local adaptation (Fig. 6) and spatial integration (Fig. 7).

General electrophysiological setup

The electrophysiological setup consisted of a differential amplifier (Model 1700, A-M Systems, Sequim, WA, USA), an oscilloscope (TBAS 1046, Tektronix, Beaverton, OR, USA) and an A/D converter (Model 118, iWorks Systems, Dover, NH, USA). Recordings were performed inside a Faraday cage on a vibration isolation table (TMC 66-501, Technical Manufacturing Corporation, Peabody, MA, USA). Data were stored on a PC using LabScribe software (iWorks), and analyzed using custom-written code in Octave (https://www.gnu.org/software/octave/). To tightly control background illumination, the entire recording area was enclosed in black-out fabric (BK5, Thorlabs, Newton, NJ, USA). In addition, the room light was kept off during experiments, so that the only light sources in the room were indicator lights on electronic equipment and a computer screen. The light seal of the recording area was tested by means of a sudden substantial increase in ambient room light after the leech was fully dark adapted. The light seal was trusted only if this did not elicit a response.

Measuring light intensity

Measurements were taken with a spectrometer (USB2000+ with a QP600-025-SR optical fiber and a CC3-UV-T cosine corrector Ocean Optics, Dunedin, FL, USA) which was calibrated against a calibrated light source (DH-2000, Ocean Optics). All reported light intensities are absolute numbers from radiometric irradiance measurements, in units of photons cm −2 s −1 . To obtain controlled light intensities below the minimum intensity that the spectrometer could directly measure, we used calibrated neutral density filters placed in front of a brighter light source. Calibration of neutral density filters was performed independently for each relevant wavelength. All measurements were made with the cosine corrector of the spectrometer probe at the same distance and orientation relative to the light source as the leech would be in our actual experiments. Although we took great care to measure light intensities as accurately as possible, it should be noted that measuring absolute light intensities accurately is notoriously challenging: according to Johnsen (2012), measurement errors up to 10% (0.1 log units) are to be expected even in the best scenarios. We believe our measurements to be accurate to about that level. Furthermore, as all of our key results rely on relative light intensities, minor errors in absolute intensity values do not affect the interpretation of our results.

Spectral sensitivity measurements

Monochromatic light was generated by coupling a 150 W xenon arc lamp (Apex 70525 Monochromator Illuminator, Oriel Instruments, Stratford, CT, USA) to a monochromator (Cornerstone 130 1/8 m 74000, Oriel). In previous experiments using this system, we had observed a small secondary peak at approximately 300 nm below the primary peak wavelength. To eliminate this secondary peak, we used a long-pass filter (ET542LP, Chroma, Bellows Falls, VT, USA) for all primary wavelengths of 590 nm and above. The light intensity was controlled with a variable neutral density filter (50Q00AV.2, Newport Corporation, Irvine, CA, USA) mounted on a motorized rotator stage (NSR-12 controlled by a NewStep NSC200 controller, both Newport Corporation). Three additional neutral density filters (FRQ-ND1 and FRQ-ND2, Newport Corporation NDUV30A, Thorlabs) that were mounted onto a manual filter wheel (FW1A, Thorlabs) were used to achieve light attenuation beyond the range of the motorized filter wheel. The duration of the stimulus was controlled with a shutter (VCM-D1, Uniblitz, Rochester, NY, USA). The light path also contained two lenses (LJ4395-UV and LA4306-UV, Thorlabs) that focused the light onto an optical fiber placed directly behind the shutter. (Lenses and fiber were chosen to transmit both UV and visible light.) At the end of the optical fiber was a lens that collimated the light so that a light spot with a diameter of 2.8–3.5 cm was projected onto the leech from a distance of 10–13 cm. The light source was positioned above the leech and illuminated the entire posterior ventral side ranging from the body wall opening at M10 to the rear sucker at an angle of no greater than 30 deg from normal.

Leeches were dark adapted for at least 30 min before starting a recording, and recordings were performed without background illumination. (We could not quantify stray background light, but estimate it to be below 10 8 photons cm −2 s −1 , or approximately 0.0002 lx, similar to the darkness under an overcast sky on a moonless night.) We recorded responses to 500-ms stimuli with the following peak wavelengths (in nm): 320, 350, 400, 455, 530, 590 and 655. The order of wavelengths that we tested was randomized. To generate response–log(intensity) curves, we used light intensities in a range of approximately 3 log units in steps of approximately 1/3 log units, always working in order of increasing light intensity, separately for each wavelength. Preliminary data (not shown) showed that it was critical to include prolonged recovery times between stimuli especially after a strong response to relatively high light intensity. To optimize the quality of obtained data, we allowed at least 1 min and up to 5 min between stimuli, depending on the stimulus light intensity and responses.

Adaptation to green and UV light

For these experiments, we used LEDs in combination with neutral density filters to achieve higher light intensities and a wider range of intensities than what was possible with the monochromator. The LEDs were controlled by a custom driver that provided a precisely regulated DC current to the LED the neutral density filters served to extend the intensity range beyond the range of the driver. We specifically did not use pulse width modulation (i.e. control of the duty cycle of flicker) to avoid assumptions about the frequency response of the visual system. Schematic diagrams are available from the corresponding author on request.

For UV, we used LEDs with a dominant wavelength of 365 nm (LED Engin LZ1-10UV00, Mouser, Mansfield, TX, USA) and the same neutral density filters as above. For green light, we used 523 nm LEDs and OD-2 and OD-4 filters (NE20B-A and NE40B-A, Thorlabs). In this way, we achieved a green background light intensity range of 6 log units and a green and UV stimulus light intensity range of approximately 7.5 log units. The UV stimulus light (but not the UV background) was fitted with a filter (357/25x, Chroma AT) that eliminated a small secondary peak within the visual wavelength range. As UV illumination elicited a strong fluorescence of the exposed intestinal tissue at the body wall opening, we removed this tissue as much as possible, and closed up the body wall opening for the recording.

Each LED was mounted behind a condenser lens (ACL2520, f=20 mm, Thorlabs). The background and stimulus LED assemblies were mounted directly above the leech such that the angle between them was no more than 15 deg. The background illuminated the leech from a distance of 19 cm the stimulus illuminated the leech from a distance of 11 cm. The illuminated area had a diameter of 9.5–10.5 cm. The leech was pinned out to a length of no more than 6 cm, so that the entire ventral side was illuminated by both the background and the stimulus (Fig. 1B). The green and UV background LEDs were mounted at fixed positions immediately adjacent to one another on a slider that allowed their positions to be switched. This ensured that the stimulus location and orientation were identical regardless of wavelength.

To quantify the adaptation to green background light, we tested six background intensities ranging from 3.4×10 10 to 3.4×10 15 photons cm −2 s −1 in steps of 1 log unit. Because the need to keep our experimental animals healthy throughout the experiment imposed time constraints on the duration of experiments, each leech (n=11) was tested with only three or four of the six background light intensities. (Specifically, we tested the lowest light level on 11 leeches, the second level on 6 leeches, the third on 4, the fourth on 3, the fifth on 5 and the highest on 10.)

As above, leeches were dark adapted for 30 min before recording, and additionally background adapted for 10 min every time we changed the background illumination or had to open the light seal to exchange neutral density filters. To generate response–log(intensity) curves for each background light intensity and stimulus wavelength (green and UV), we applied 2-s stimuli with intensities spanning 3 log units in steps of approximately 1/4 log units, in order of increasing light intensity. To prevent adaptation to the stimulus intensity, 3 min of only background illumination was provided between stimuli.

Local versus non-local adaptation

Two green through-hole LEDs (941-C505BGANCC0D0781, Mouser) provided differential background illumination to the anterior and posterior halves of the leech. A third such LED delivered flash stimuli to the posterior half of the leech. All LEDs were mounted at a distance of 9 cm from the leech the stimulus LED was mounted immediately adjacent to the LED that provided background illumination to the posterior half of the animal. A light barrier consisting of blackout fabric was placed between the anterior and posterior halves of the leech to ensure controlled differential stimulation of the two halves (Fig. 1C). As above, we used neutral density filters to reduce light intensity beyond the range of the LEDs. These were mounted onto a slider so that they could be exchanged from the outside without opening the light seal of the recording area.

Two levels of background light intensity were used in these experiments: 3.9×10 12 photons cm −2 s −1 (‘dark’) and 4.4×10 13 photons cm −2 s −1 (‘light’). All combinations of light and dark background conditions were tested, always in the following order: (1) both halves dark (2) both halves light (3) posterior light, anterior dark (4) posterior dark, anterior light (5) both halves dark (as a control to test whether we could recover the initial response). For constructing response curves, the same range, step size, order of stimulation and stimulus duration were used as for the previous experiment.

Spatial integration

Background illumination intensity was 4.5×10 11 photons cm −2 s −1 . The setup was otherwise the same as for the local versus non-local adaptation experiment, except that an additional stimulus LED was used to provide flashes to the anterior region. Order of stimulation was: (1) anterior only (2) anterior and posterior together (3) anterior only again to test whether we could recover the initial responses. After that, we cut the cord posterior to the recording site, which disconnected the posterior half of the body from our recording site, and tested for the influence of stray light by stimulating (4) posterior only (which potentially could affect the anterior side through stray light) and (5) anterior only, to test whether initial responses could be recovered. Stimulus duration, intensity range, step size, order of stimulation and time between stimuli were as before.

Data analysis

S-cell responses to light stimulation and spectral sensitivity. (A) Responses to 2-s flashes of green light (530 nm, 1.5×10 11 photons cm −2 s −1 shaded area) presented to the posterior half of the ventral body wall. Top to bottom: representative raw extracellular trace raster plots from 20 individual trials on a single leech firing rate histogram of those trials. Scale bars: 1 s and 25 spikes s −1 . (B) Response curves to 500-ms flashes of light of various wavelengths (one representative leech). (C) Spectral sensitivity of S-cell responses (I50, light intensity for 50% response). Dots represent individual animals black lines mark means and s.e.m. Letters mark groupings from ANOVA/Tukey (at P<0.05 n=5).

S-cell responses to light stimulation and spectral sensitivity. (A) Responses to 2-s flashes of green light (530 nm, 1.5×10 11 photons cm −2 s −1 shaded area) presented to the posterior half of the ventral body wall. Top to bottom: representative raw extracellular trace raster plots from 20 individual trials on a single leech firing rate histogram of those trials. Scale bars: 1 s and 25 spikes s −1 . (B) Response curves to 500-ms flashes of light of various wavelengths (one representative leech). (C) Spectral sensitivity of S-cell responses (I50, light intensity for 50% response). Dots represent individual animals black lines mark means and s.e.m. Letters mark groupings from ANOVA/Tukey (at P<0.05 n=5).

Adaptation to intensity of background light. (A) Intensity of green stimulus light required to attain 50% of the plateau response (I50, see Materials and Methods) as a function of green background intensity. Symbols indicate animals lines are linear fits for each animal. (B) Intensity of UV stimulus light required to attain the same response as in A as a function of green background intensity. Lines are linear fits separately for the low-background (left) and high-background (right) regimes. (C) Difference in light intensity required to attain 50% of the plateau response when using UV light versus green light, at the lowest background (b/g) intensity (left) and at the highest background intensity (right). ***P<10 –7 , t-test (n=11). (D) Summary of fit results from A and B. From left to right, slope of the response curve to green light (Green), to UV light in the low-background regime (UV, low b/g) and to UV light in the high-background regime (UV, high b/g). Black dots indicate the slopes of individual fits bars indicate mean and s.d. across animals. ***P<10 –5 , t-test (n=8). (E,F) Delay of the response to green and UV light stimulation at the lowest background light intensity (E) and highest background light intensity (F). The stimulus light intensity is plotted normalized to I50. Symbols indicate individual leeches, lines are fits for each animal and the dashed line indicates the light intensity that elicited half-maximum response (I50). (G) Summary of the data from E and F, showing the delay of the response at I50 for green and UV stimulation at the lowest (left) and highest (right) background light intensity. ***P<10 –5 , t-test (n=11).

Adaptation to intensity of background light. (A) Intensity of green stimulus light required to attain 50% of the plateau response (I50, see Materials and Methods) as a function of green background intensity. Symbols indicate animals lines are linear fits for each animal. (B) Intensity of UV stimulus light required to attain the same response as in A as a function of green background intensity. Lines are linear fits separately for the low-background (left) and high-background (right) regimes. (C) Difference in light intensity required to attain 50% of the plateau response when using UV light versus green light, at the lowest background (b/g) intensity (left) and at the highest background intensity (right). ***P<10 –7 , t-test (n=11). (D) Summary of fit results from A and B. From left to right, slope of the response curve to green light (Green), to UV light in the low-background regime (UV, low b/g) and to UV light in the high-background regime (UV, high b/g). Black dots indicate the slopes of individual fits bars indicate mean and s.d. across animals. ***P<10 –5 , t-test (n=8). (E,F) Delay of the response to green and UV light stimulation at the lowest background light intensity (E) and highest background light intensity (F). The stimulus light intensity is plotted normalized to I50. Symbols indicate individual leeches, lines are fits for each animal and the dashed line indicates the light intensity that elicited half-maximum response (I50). (G) Summary of the data from E and F, showing the delay of the response at I50 for green and UV stimulation at the lowest (left) and highest (right) background light intensity. ***P<10 –5 , t-test (n=11).

Adaptation to the spectrum of background light. (A) Response to stimuli with green light (greens) and UV light (purples) on a background of either green light (circles) or UV light (crosses). Background intensity was 3.4×10 15 photons cm −2 s −1 for the green background and 9.7×10 15 photons cm −2 s −1 for the UV background (see Results, Physiological evidence for a second color channel, for rationale). Filled and open purple markers represent data collected under the same conditions at the beginning and end of the experiment, to confirm stability of responses. Data from one representative animal. (B) Stimulus light intensity required to elicit a response at least 35% as strong as the plateau response for UV stimuli on the green background (I35). ***P<0.0001, Tukey test following ANOVA (F3,15=32.5, P<10 –6 , n=6 leeches). Colors as in A.

Adaptation to the spectrum of background light. (A) Response to stimuli with green light (greens) and UV light (purples) on a background of either green light (circles) or UV light (crosses). Background intensity was 3.4×10 15 photons cm −2 s −1 for the green background and 9.7×10 15 photons cm −2 s −1 for the UV background (see Results, Physiological evidence for a second color channel, for rationale). Filled and open purple markers represent data collected under the same conditions at the beginning and end of the experiment, to confirm stability of responses. Data from one representative animal. (B) Stimulus light intensity required to elicit a response at least 35% as strong as the plateau response for UV stimuli on the green background (I35). ***P<0.0001, Tukey test following ANOVA (F3,15=32.5, P<10 –6 , n=6 leeches). Colors as in A.

Transcriptome analyses to identify opsins

Transcriptomic databases were generated from two separate tissue types: (1) a single head containing the eyes and (2) 100 isolated sensilla collected from the body. Tissues were dissected in ice-cold RNAse-free Gibco PBS (Thermo Fisher Scientific, Waltham, MA, USA). Tissues were briefly frozen in liquid nitrogen and ground using a mortar and pestle. RNA isolation was conducted using the RNeasy Lipid Tissue Kit (Qiagen, Valencia, CA, USA). To assess the quality of the RNA, extractions were subjected to spectrophotometric analysis utilizing a NanoDrop 1000 Spectrometer (Thermo Fisher Scientific) where the A260/280 absorbance ratio yielded measurements around 2.0 for RNA extracts, indicating that all RNA measurements were relatively pure. RNA-seq utilized the Illumina HiSeq 2500 (75 bp) with Ribo-zero preparation at Cincinnati Children's Hospital Core Sequencing Facility (Cincinnati, OH, USA). The raw read FASTQ files were assembled using Trinity (Grabherr et al., 2011), CLC Genomics and Oases (Schulz et al., 2012) according to previously described methods (Rosendale et al., 2016). Expression was assessed by mapping reads based on parameters described in Rosendale et al. (2016). The quality of each transcriptome was assessed through evaluation of the Benchmarking Universal Single-Copy Orthologs (BUSCO) gene sets (Simão et al., 2015).

Opsin sequences were identified using the Blastx algorithm (Altschul et al., 1997) to identify orthologs to the previously annotated opsin sequences of H. robusta (Döring et al., 2013) along with opsin sets obtained from arthropod and other invertebrate species from NCBI nr databases. These two different databases were used to identify potential functionality, as many annelid-specific opsins have not been fully characterized. A reciprocal BLAST against the invertebrate and arthropod databases was used to confirm whether predicted genes match opsins in other systems. Relationships between the opsin sequences and contigs were assessed through the use of MEGA5 (Tamura et al., 2011) to generate a neighbor joining tree after sequence alignment with CLUSTAL Omega (Sievers and Higgins, 2014). Illumina sequencing files have been deposited in NCBI SRA (Bioproject: PRJNA504032).


Contents

The first person credited with being employed as a science teacher in a British public school was William Sharp, who left the job at Rugby School in 1850 after establishing science to the curriculum. Sharp is said to have established a model for science to be taught throughout the British public school system. [1]

The British Academy for the Advancement of Science (BAAS) published a report in 1867 [2] calling for the teaching of "pure science" and training of the "scientific habit of mind." The progressive education movement supported the ideology of mental training through the sciences. BAAS emphasized separately pre-professional training in secondary science education. In this way, future BAAS members could be prepared.

The initial development of science teaching was slowed by the lack of qualified teachers. One key development was the founding of the first London School Board in 1870, which discussed the school curriculum another was the initiation of courses to supply the country with trained science teachers. In both cases the influence of Thomas Henry Huxley. John Tyndall was also influential in the teaching of physical science. [3]

In the United States, science education was a scatter of subjects prior to its standardization in the 1890s. [4] The development of a science curriculum emerged gradually after extended debate between two ideologies, citizen science and pre-professional training. As a result of a conference of thirty leading secondary and college educators in Florida, the National Education Association appointed a Committee of Ten in 1892, which had authority to organize future meetings and appoint subject matter committees of the major subjects taught in secondary schools. The committee was composed of ten educators and chaired by Charles Eliot of Harvard University. The Committee of Ten appointed nine conferences committees: Latin Greek English Other Modern Languages Mathematics History Civil Government and Political Economy physics, astronomy, and chemistry natural history and geography. Each committee was composed of ten leading specialists from colleges, normal schools, and secondary schools. Committee reports were submitted to the Committee of Ten, which met for four days in New York City, to create a comprehensive report. [5] In 1894, the NEA published the results of work of these conference committees. [5]

According to the Committee of Ten, the goal of high school was to prepare all students to do well in life, contributing to their well-being and the good of society. Another goal was to prepare some students to succeed in college. [6]

This committee supported the citizen science approach focused on mental training and withheld performance in science studies from consideration for college entrance. [7] The BAAS encouraged their longer standing model in the UK. [8] The US adopted a curriculum was characterized as follows: [5]

  • Elementary science should focus on simple natural phenomena (nature study) by means of experiments carried out "in-the-field."
  • Secondary science should focus on laboratory work and the committee's prepared lists of specific experiments
  • Teaching of facts and principles
  • College preparation

The format of shared mental training and pre-professional training consistently dominated the curriculum from its inception to now. However, the movement to incorporate a humanistic approach, such as inclusion of the arts (S.T.E.A.M.), science, technology, society and environment education is growing and being implemented more broadly in the late 20th century. Reports by the American Academy for the Advancement of Science (AAAS), including Project 2061, and by the National Committee on Science Education Standards and Assessment detail goals for science education that link classroom science to practical applications and societal implications.

Science is a universal subject that spans the branch of knowledge that examines the structure and behavior of the physical and natural world through observation and experiment. [9] Science education is most commonly broken down into the following three fields: Biology, Chemistry, and Physics.

Physics education Edit

Physics education is characterized by the study of science that deals with matter and energy, and their interactions. [10]

Physics First, a program endorsed by the American Association of Physics Teachers, is a curriculum in which 9th grade students take an introductory physics course. The purpose is to enrich students' understanding of physics, and allow for more detail to be taught in subsequent high school biology and chemistry classes. It also aims to increase the number of students who go on to take 12th grade physics or AP Physics, which are generally elective courses in American high schools. [22]

Physics education in high schools in the United States has suffered the last twenty years because many states now only require three sciences, which can be satisfied by earth/physical science, chemistry, and biology. The fact that many students do not take physics in high school makes it more difficult for those students to take scientific courses in college.

At the university/college level, using appropriate technology-related projects to spark non-physics majors' interest in learning physics has been shown to be successful. [23] This is a potential opportunity to forge the connection between physics and social benefit.

Chemistry education Edit

Chemistry education is characterized by the study of science that deals with the composition, structure, and properties of substances and the transformations that they undergo. [11]

Chemistry is the study of chemicals and the elements and their effects and attributes. Students in chemistry learn the periodic table. The branch of science education known as "chemistry must be taught in a relevant context in order to promote full understanding of current sustainability issues." [12] As this source states chemistry is a very important subject in school as it teaches students to understand issues in the world. As children are interested by the world around them chemistry teachers can attract interest in turn educating the students further. [13] The subject of chemistry is a very practical based subject meaning most of class time is spent working or completing experiments.

Biology education Edit

Biology education is characterized by the study of structure, function, heredity, and evolution of all living organisms. [14] Biology itself is the study of living organisms, through different fields including morphology, physiology, anatomy, behavior, origin, and distribution. [15]

Depending on the country and education level, there are many approaches to teaching biology. In the United States, there is a growing emphasis on the ability to investigate and analyze biology related questions over an extended period of time. [16]

While the public image of science education may be one of simply learning facts by rote, science education in recent history also generally concentrates on the teaching of science concepts and addressing misconceptions that learners may hold regarding science concepts or other content. Thomas Kuhn, whose 1962 book The Structure of Scientific Revolutions greatly influenced the post-positivist philosophy of science, argued that the traditional method of teaching in the natural sciences tends to produce a rigid mindset. [17] [18]

Since the 1980s, science education has been strongly influenced by constructivist thinking. [19] [20] [21] Constructivism in science education has been informed by an extensive research programme into student thinking and learning in science, and in particular exploring how teachers can facilitate conceptual change towards canonical scientific thinking. Constructivism emphasises the active role of the learner, and the significance of current knowledge and understanding in mediating learning, and the importance of teaching that provides an optimal level of guidance to learners. [22]

Guided-discovery approach Edit

Along with John Dewey, Jerome Bruner, and many others, Arthur Koestler [23] offers a critique of contemporary science education and proposes its replacement with the guided-discovery approach:

To derive pleasure from the art of discovery, as from the other arts, the consumer—in this case the student—must be made to re-live, to some extent, the creative process. In other words, he must be induced, with proper aid and guidance, to make some of the fundamental discoveries of science by himself, to experience in his own mind some of those flashes of insight which have lightened its path. . . . The traditional method of confronting the student not with the problem but with the finished solution, means depriving him of all excitement, [shutting] off the creative impulse, [reducing] the adventure of mankind to a dusty heap of theorems.

Specific hands-on illustrations of this approach are available. [24] [25]

The practice of science education has been increasingly informed by research into science teaching and learning. Research in science education relies on a wide variety of methodologies, borrowed from many branches of science and engineering such as computer science, cognitive science, cognitive psychology and anthropology. Science education research aims to define or characterize what constitutes learning in science and how it is brought about.

John D. Bransford, et al., summarized massive research into student thinking as having three key findings:

Preconceptions Prior ideas about how things work are remarkably tenacious and an educator must explicitly address a students' specific misconceptions if the student is to reconfigure his misconception in favour of another explanation. Therefore, it is essential that educators know how to learn about student preconceptions and make this a regular part of their planning. Knowledge organization In order to become truly literate in an area of science, students must, "(a) have a deep foundation of factual knowledge, (b) understand facts and ideas in the context of a conceptual framework, and (c) organize knowledge in ways that facilitate retrieval and application." [26] Metacognition Students will benefit from thinking about their thinking and their learning. They must be taught ways of evaluating their knowledge and what they don't know, evaluating their methods of thinking, and evaluating their conclusions. Some educators and others have practiced and advocated for discussions of pseudoscience as a way to understand what it is to think scientifically and to address the problems introduced by pseudoscience. [27] [28]

Educational technologies are being refined to meet the specific needs of science teachers. One research study examining how cellphones are being used in post-secondary science teaching settings showed that mobile technologies can increase student engagement and motivation in the science classroom. [29]

According to a bibliography on constructivist-oriented research on teaching and learning science in 2005, about 64 percent of studies documented are carried out in the domain of physics, 21 percent in the domain of biology, and 15 percent in chemistry. [30] The major reason for this dominance of physics in the research on teaching and learning appears to be that understanding physics includes difficulties due to the particular nature of physics. [31] Research on students' conceptions has shown that most pre-instructional (everyday) ideas that students bring to physics instruction are in stark contrast to the physics concepts and principles to be achieved – from kindergarten to the tertiary level. Quite often students' ideas are incompatible with physics views. [32] This also holds true for students' more general patterns of thinking and reasoning. [33] [34] [35]

Australia Edit

As in England and Wales, science education in Australia is compulsory up until year 11, where students can choose to study one or more of the branches mentioned above. If they wish to no longer study science, they can choose none of the branches. The science stream is one course up until year 11, meaning students learn in all of the branches giving them a broad idea of what science is all about. The National Curriculum Board of Australia (2009) stated that "The science curriculum will be organised around three interrelated strands: science understanding science inquiry skills and science as a human endeavour." [36] These strands give teachers and educators the framework of how they should be instructing their students.

In 2011, it was reported that a major problem that has befallen science education in Australia over the last decade is a falling interest in science. Fewer year 10 students are choosing to study science for year 11, which is problematic as these are the years where students form attitudes to pursue science careers. [37] This issue is not unique in Australia, but is happening in countries all over the world.

China Edit

Educational quality in China suffers because a typical classroom contains 50 to 70 students. With over 200 million students, China has the largest educational system in the world. However, only 20% percent of students complete the rigorous ten-year program of formal schooling. [38]

As in many other countries, the science curriculum includes sequenced courses in physics, chemistry, and biology. Science education is given high priority and is driven by textbooks composed by committees of scientists and teachers. Science education in China places great emphasis on memorization, and gives far less attention to problem solving, application of principles to novel situations, interpretations, and predictions. [38]

United Kingdom Edit

In English and Welsh schools, science is a compulsory subject in the National Curriculum. All pupils from 5 to 16 years of age must study science. It is generally taught as a single subject science until sixth form, then splits into subject-specific A levels (physics, chemistry and biology). However, the government has since expressed its desire that those pupils who achieve well at the age of 14 should be offered the opportunity to study the three separate sciences from September 2008. [39] In Scotland the subjects split into chemistry, physics and biology at the age of 13–15 for National 4/5s in these subjects, and there is also a combined science standard grade qualification which students can sit, provided their school offers it.

In September 2006 a new science program of study known as 21st Century Science was introduced as a GCSE option in UK schools, designed to "give all 14 to 16-year-old's a worthwhile and inspiring experience of science". [40] In November 2013, Ofsted's survey of science [41] in schools revealed that practical science teaching was not considered important enough. [42] At the majority of English schools, students have the opportunity to study a separate science program as part of their GCSEs, which results in them taking 6 papers at the end of Year 11 this usually fills one of their option 'blocks' and requires more science lessons than those who choose not to partake in separate science or are not invited. Other students who choose not to follow the compulsory additional science course, which results in them taking 4 papers resulting in 2 GCSEs, opposed to the 3 GCSEs given by taking separate science.

United States Edit

In many U.S. states, K-12 educators must adhere to rigid standards or frameworks of what content is to be taught to which age groups. This often leads teachers to rush to "cover" the material, without truly "teaching" it. In addition, the process of science, including such elements as the scientific method and critical thinking, is often overlooked. This emphasis can produce students who pass standardized tests without having developed complex problem solving skills. [43] Although at the college level American science education tends to be less regulated, it is actually more rigorous, with teachers and professors fitting more content into the same time period. [44]

In 1996, the U.S. National Academy of Sciences of the U.S. National Academies produced the National Science Education Standards, which is available online for free in multiple forms. Its focus on inquiry-based science, based on the theory of constructivism rather than on direct instruction of facts and methods, remains controversial. [44] Some research suggests that it is more effective as a model for teaching science.

"The Standards call for more than 'science as process,' in which students learn such skills as observing, inferring, and experimenting. Inquiry is central to science learning. When engaging in inquiry, students describe objects and events, ask questions, construct explanations, test those explanations against current scientific knowledge, and communicate their ideas to others. They identify their assumptions, use critical and logical thinking, and consider alternative explanations. In this way, students actively develop their understanding of science by combining scientific knowledge with reasoning and thinking skills." [45]

Concern about science education and science standards has often been driven by worries that American students, and even teachers, [46] lag behind their peers in international rankings. [47] One notable example was the wave of education reforms implemented after the Soviet Union launched its Sputnik satellite in 1957. [48] The first and most prominent of these reforms was led by the Physical Science Study Committee at MIT. In recent years, business leaders such as Microsoft Chairman Bill Gates have called for more emphasis on science education, saying the United States risks losing its economic edge. [49] To this end, Tapping America's Potential is an organization aimed at getting more students to graduate with science, technology, engineering and mathematics degrees. [50] Public opinion surveys, however, indicate most U.S. parents are complacent about science education and that their level of concern has actually declined in recent years. [51]

Furthermore, in the recent National Curriculum Survey conducted by ACT, researchers uncovered a possible disconnect among science educators. "Both middle school/junior high school teachers and post secondary science instructors rate(d) process/inquiry skills as more important than advanced science content topics high school teachers rate them in exactly the opposite order." Perhaps more communication among educators at the different grade levels in necessary to ensure common goals for students. [52]

2012 science education framework Edit

According to a report from the National Academy of Sciences, the fields of science, technology, and education hold a paramount place in the modern world, but there are not enough workers in the United States entering the science, technology, engineering, and math (STEM) professions. In 2012 the National Academy of Sciences Committee on a Conceptual Framework for New K-12 Science Education Standards developed a guiding framework to standardize K-12 science education with the goal of organizing science education systematically across the K-12 years. Titled A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas, the publication promotes standardizing K-12 science education in the United States. It emphasizes science educators to focus on a "limited number of disciplinary core ideas and crosscutting concepts, be designed so that students continually build on and revise their knowledge and abilities over multiple years, and support the integration of such knowledge and abilities with the practices needed to engage in scientific inquiry and engineering design." [53]

The report says that in the 21st century Americans need science education in order to engage in and "systematically investigate issues related to their personal and community priorities," as well as to reason scientifically and know how to apply science knowledge. The committee that designed this new framework sees this imperative as a matter of educational equity to the diverse set of schoolchildren. Getting more diverse students into STEM education is a matter of social justice as seen by the committee. [54]

2013 Next Generation Science Standards Edit

In 2013 a new standards for science education were released that update the national standards released in 1996. Developed by 26 state governments and national organizations of scientists and science teachers, the guidelines, called the Next Generation Science Standards, are intended to "combat widespread scientific ignorance, to standardize teaching among states, and to raise the number of high school graduates who choose scientific and technical majors in college. " Included are guidelines for teaching students about topics such as climate change and evolution. An emphasis is teaching the scientific process so that students have a better understanding of the methods of science and can critically evaluate scientific evidence. Organizations that contributed to developing the standards include the National Science Teachers Association, the American Association for the Advancement of Science, the National Research Council, and Achieve, a nonprofit organization that was also involved in developing math and English standards. [55] [56]


Table of Contents

1 Biology of the Chameleons: An Introduction
Krystal A. Tolley and Anthony Herrel

2 Chameleon Anatomy
Christopher V. Anderson and Timothy E. Higham
2.1 Musculoskeletal Morphology
2.2 External Morphology and Integument
2.3 Sensory Structures
2.4 Visceral Systems

3 Chameleon Physiology
Anthony Herrel
3.1 Neurophysiology
3.2 Muscle Physiology
3.3 Metabolism, Salt, and Water Balance
3.4 Temperature
3.5 Skin Pigmentation, Color Change, and the Role of Ultraviolet Light
3.6 Developmental Physiology

4 Function and Adaptation of Chameleons
Timothy E. Higham and Christopher V. Anderson
4.1 Locomotion
4.2 Feeding

5 Ecology and Life History of Chameleons
G. John Measey, Achille Raselimanana, and Anthony Herrel
5.1 Habitat
5.2 Life-History Traits
5.3 Foraging and Diet
5.4 Predators

6 Chameleon Behavior and Color Change
Devi Stuart-Fox
6.1 Sensory Systems and Modes of Communication
6.2 Color Changes
6.3 Social and Reproductive Behavior
6.4 Sexual Dimorphism: Body Size and Ornamentation
6.5 Antipredator Behavior

7 Evolution and Biogeography of Chameleons
Krystal A. Tolley and Michele Menegon
7.1 Evolutionary Relationships
7.2 Diversity and Distribution
7.3 Regional Diversity
7.4 Patterns of Alpha Diversity
7.5 Patterns of Beta Diversity

8 Overview of the Systematics of the Chamaeleonidae
Colin R. Tilbury
8.1 Evolution of Methodology in Chameleon Taxonomy
8.2 Current Status of Taxonomy of the Chamaeleonidae
8.3 Subfamilial Groupings within Chamaeleonidae
8.4 Overview of Extant Genera

9 Fossil History of Chameleons
Arnau Bolet and Susan E. Evans
9.1 Phylogenetic Relationships of Iguania and Acrodonta
9.2 Fossil Record of Acrodonta
9.3 Origins of Acrodonta
9.4 Origins of Chamaeleonidae

10 Chameleon Conservation
Richard Jenkins, G. John Measey, Christopher V. Anderson, and Krystal A. Tolley
10.1 Conservation Status of Chameleons
10.2 Trade in Chameleons
10.3 Chameleons and Global Change
10.4 The Way Forward

Appendix
Abbreviations
References
Photo Credits
Index


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