Biology h

For all degree programs within the Department of Natural Sciences, no on-line classes will be accepted in place of face- to-face courses with laboratories. Students can file for an exception with the Department Chair if it can be demonstrated that all 3 of the following conditions have been met: The required science class was not offered at least TWO times over the course of a standard eight-semester college experience. The student can provide documentation of the conflict(s) that prevented enrollment in the face-to-face course when it was offered. The student can provide evidence that they have met with and followed the recommendations of their appropriate, assigned post-freshman advisor prior to the required course offerings.

BIOL 138& 138LGENERAL BIOLOGY: BOTANYand GENERAL BIOLOGY: BOTANY LABORATORY4 BIOL 139& 139LGENERAL BIOLOGY: ZOOLOGYand GENERAL BIOLOGY: ZOOLOGY LABORATORY4

BIOL 315. Genetics. 3 Credits. An introduction to genetics, with emphasis on classical genetic analysis and the biochemistry of gene transmission, expression and regulation. Prerequisites: BIOL 150, BIOL 150L, BIOL 151, and BIOL 151L or an equivalent approved by the department. F.

Students who wish to challenge the rejection of credit for course equivalency, general education, or program credit may request an additional review by the Office of Academic Records or the appropriate department chair.  Students requesting an additional review are responsible for providing supporting evidence.

if turnover is fast the accumulation of respiring biomass is low and respiration depends primarily on photosynthesis; while if turnover is slow the accumulation of respiring biomass is high and respiration depends primarily on biomass

Students are required to take one additional course of three or more credits from the General Education curriculum 

Institutional Specific (must be chosen from one of the following four categories: communication, social sciences, arts and humanities, and/or mathematics/science & technology)

Mathematics, Science & Technology

Arts & Humanities

Communications

Social Sciences

403.7 Common General Education Requirement and Transfer of General Education Credits

A stomatal safety-efficiency trade-off constrains responses to leaf dehydration

Accessing a Single Value from Variables

Photosystem I that is ready to accept electrons

One or all of the acceptors of Photosystem I have no electron(s).

All the acceptor side of Photosystem I are occupied by electrons and cannot accept any more electrons. Kanazawa et al. Front. Plant Sci. (2017)

Active Photosystem I that is operational to receive/pass electrons.

PSIox i

PSI over-reduced (PSIor),

PSIopen

The total active PSI centers (PSIact) in the leaves under a certain condition is proportional to PM, the maximal absorption difference between dark and the second saturation pulse taken after application of far red light to oxidize electron carriers. It was assumed that all PSI centers in dark adapted material (before light treatments) were active, so the all parameters were normalized to the Po, PM value measured in dark adapted leaves prior to illumination with a full complement of active PSI centers. Thus, for example, the fraction of active PSI, PSIact is expressed as the ratio of PM/P0, where P0, is the PM value measured in dark adapted leaves prior to illumination with a full complement of active PSI centers.

Variety collinsii: Stem leaves with heart-shaped bases that often clasp the stem. Petals less than 7 mm long. Pedicels bent sharply downwards at their base. The siliques are more or less straight. Found from Washington to Alberta, Wyoming and east through he Dakotas and Manitoba to Quebec.

Grading Rubric

100

phyB

"protocolrepeats"

"protocols": 12,

"protocols_delay": 300000

300000

"environmental": [

e "averages",

wiki on github

Such losses have also occurred in embryophytes, adding to the complexity of trying to define these lineages in functional terms. While oxygenic photosynthesis is monophyletic, the eukaryotic algae are polyphyletic.

10-pin point

0.3 mM CaCl2

The Gibberellin Signalling Pathway

The Brassinosteroid Perception Pathway

The Auxin Response Pathway

Figure 1Examples of auxin, gibberellin or brassinosteroid involvement in growth phenomena across the plant life cycle.

only cytokinin, auxin, gibberellins and brassinosteroids are considered to be essential for growth.

abscisic acid, auxin, brassinosteroids, cytokinins, ethylene, gibberellins, jasmonates and strigolactones

To demonstrate that P deficiency in plants is highly reversible and that disruptions in electron transport can be recovered rapidly, we infiltrated P-deficient leaf segments with a Pi-containing solution by immersion for 60 min.

The objective of this study was to develop a comprehensive biological model of how photosynthesis is affected by P deficiency under physiologically relevant conditions.

This obviously low P use efficiency is unsustainable.

Multiple sets of barley plants (Hordeum vulgare ‘Quench’) were hydroponically cultivated using three different treatments:

It has been estimated that 30% of the world’s arable soils are deficient in P and require P fertilization to improve yields (MacDonald et al., 2011).

To test this hypothesis we conducted a detailed study on the root architecture of these crops using SimRoot (Postma and Lynch, 2011a, b), a functional–structural plant model, and estimated competition for nitrate, potassium and phosphorus among roots of maize, bean and squash plants grown in monoculture or polyculture.

Maize, bean and squash differ strongly in root architecture (Weaver and Bruner, 1927) and we hypothesize that these differences in root architecture allow these crops to explore different soil domains with variable intensity

Root architecture, however, has been overlooked in intercropping studies despite the recognition that root placement may be more important for competition than root physiology (Schwinning and Weiner, 1998).

The presence of highly pitted lignified tissue in the mesophyll of gymnosperms leaves has been formally noted in the conifer family Podocarpaceae and the cycad genus Cycas (Griffith, 1957; Hu and Yao, 1981). We found that similar tissues are present in conifers from all families including Sciadopitys and Amentotaxus (T. Brodribb, unpublished data) and in each case they were associated with leaf widths in excess of those achievable with unmodified mesophyll tissue (Fig. 1B). Indeed it appears that terrestrial plants have adopted two different systems to overcome the intrinsically low hydraulic conductivity of the leaf mesophyll. The most common of these is to branch the vein system such that a high volume apoplastic flow pathway (the xylem) is allowed to approach very close to the sites of evaporation. This is the means of water distribution in most angiosperm leaves. The second system, identified here, is to modify the mesophyll by directing the lignification and apoptosis (Griffith, 1957) of a proportion of mesophyll cells, thereby greatly increasing its conductivity to water. This fascinating divergence in leaf water distribution systems appears to have arisen in the gymnosperm clade, as there have been no reports of lignified mesophyll cells in any plant groups basal to gymnosperms.

We found that the photosynthetic capacity of leaves in terrestrial plants is strongly correlated with proximity of veins to the evaporative surfaces of the leaf.

yet the response of Kleaf to mean maximum mesophyll path length (Dm) fell into two distinct groups.

an intimate association between light-saturated net CO2 assimilation rate (Amax) and the hydraulic conductance (Kleaf) of whole leaves was found

B, Dm from the end of the vein xylem to the gas-exchange epidermis plotted against 1/Kleaf. Means for both parameters are shown for single-vein (white circles) and multivein (red triangles) leaves plotted together, excluding the species with lignified sclereids in the mesophyll.

A, Kleaf versus Amax in leaves of bryophytes (black), lycopods (white), ferns (green), conifers (red), angiosperms (blue), and gymnosperms with lignified sclereids in the mesophyll (brown).

In this study we examine how the water transport and photosynthetic carbon assimilation rates of leaves are related to the spatial arrangement of veins in the leaf mesophyll.

Our a priori hypothesis was that the length of mesophyll tissue that must be traversed as the transpiration stream passes from a vein ending to site of evaporation will reflect both the hydraulic and coupled photosynthetic performance of any leaf.

While our knowledge of the molecular and developmental processes that guide leaf vein development and patterning grows at an ever-increasing rate (Kang and Dengler, 2004; Fleming, 2005; Scarpella et al., 2006; Sieburth and Deyholos, 2006), the underlying physical principles that connect vein pattern with leaf productivity remain unresolved.

Leaves have sustained virtually all terrestrial ecosystems over the last 400 million years

Live- stock may be given access to the largest of these two mesas in the near future. Attempts had previously been made to construct a stock trail to its top; these efforts were being renewed in 1956

Knowing that other animals are as smart as us means we can appreciate them more, which could also help us to help them.

Selective Use of the Primary Literature Transforms the Classroom Into a Virtual Laboratory

Think of the next experiment:

Analyze and interpret the data:

http://www.genetics.org/supplemental/)

Elucidate the hypotheses:

Read:

Consider

-0.660

Seedlings of these species require large amounts of light and moisture to survive. Typically these requirements are met only in locations disturbed and irrigated by the river (Scott et al. 1996). S

Flow and Climate

Although cottonwood forests dominate river floodplains in dryregions of North America, Asia, Europe and Africa, naturally reproducing examples like the forest at THRO are increasingly rare.

This report summarizes research conducted by the U.S. Geological Survey from 2003 through 2016 on factors controlling reproduction and survival of plains cottonwood at the North and South Units of THRO (Figure1), and is relevant to management of cottonwood-dominated forests throughout the western United States.

An outstanding feature of Theodore Roosevelt National Park (THRO) is the exceptionally old and undisturbed gallery forest of plains cottonwood (Populus deltoidessubsp. monilifera) along the Little Missouri River. THRO protects the oldest known plains cottonwoods in the world, established as early as the year 1641 and growing up to 1.66 m (5.45 ft) in diameter. As the largest and most abundant tree in theriparian ecosystem, cottonwoods provide important habitat for many other species (Brinson et al. 1981).

Our results suggest that tooth size, shape, and number within some, but not all, species are sensitive to climate.

The average area of individual teeth increases with warmer temperatures in both species (Tables 2 and 3); this is opposite to the site mean observations of Royer et al. (2005).

The patterns for Q. kelloggii are more complex.

There are many significant correlations in A. rubrum between MAT and leaf physiognomy

Quercus kelloggii

Acer rubrum

in an effort to more firmly ascertain the influence of climate on leaf physiognomy within species, we report results from a large data set that includes two North American woody plants (A. rubrum and Q. kelloggii) whose native ranges span large MAT gradients and are not closely related to each other.

Investigating the role of intraspecific variation in leaf–climate relationships is important for at least three reasons

how tooth size, shape, and number respond to climate within species.

Hydathodes

However, intraspecific patterns also provide useful information

In this study, we examined the strength of correlation between leaf size and shape (physiognomy) and climate for two North American species with broad climatic ranges, Acer rubrum (red maple, Sapindaceae) and Quercus kelloggii (California black oak, Fagaceae). We sampled Q. kelloggii across a large elevation gradient (146–2362 m) but restricted sampling of A. rubrum to lowland areas (< 250 m).

Araucaria heterophylla

. The dynamic response of stomata or gs to fluctuations in light intensity has been studied in several understorey forest-dwelling species, but relatively few reports have studied crop species (Chazdon and Pearcy, 1986; Chazdon, 1991; Tinoco-Ojanguren and Pearcy, 1993; Leakey et al., 2005; McAusland et al., 2016).

Efforts to develop a big data approach to photosynthetic phenomics by recruiting many researchers into online cloud-based initiatives (Kuhlgert et al., 2016) may be promising because not only can they assay many genotypes but they can also do so under the diverse conditions which plants experience in nature.

However, the importance of the dynamic responses of photosynthesis raises a key problem that has not been adequately addressed: it is difficult to capture photosynthetic responses within (rapidly) fluctuating environments, especially in the field.

Whilst morphological adaptations to such extreme temperature fluctuations are well documented, the physiological adjustments are not (Hedberg, 1970).

Indeed, it is particularly important that light is accurately tracked by the plant for optimal photosynthetic performance

‘photosynthome’

Indeed, we are beginning to understand that the way in which photosynthesis is regulated in response to fluctuations in the environment is perhaps a more important determinant of plant productivity than its performance under steady-state or temporarily steady-state conditions

Wemeasure leaf-margin photosynthesis and transpiration througha growing season for two groups of native woody speciesfrom Pennsylvania and North Carolina.

Why are leaves more likelyto have teeth in colder climates?

Given the wide application of this proxy, calledleaf-margin analysis, it is surprising that the selective mecha-nisms driving the response of leaf margins to temperature areonly poorly known

Precipitation is limited in southwestern North Dakota

High Plains has been estimated at $38 million annually

Citizen Science and Climate Change: Mapping the Range Expansions of Native and Exotic Plants with the Mobile App Leafsnap

An Arabidopsis rbcs1a rbcs2b mutant (double mutant 1a2b) was generated by crossing T-DNA insertion lines GABI_608F01 (At1g67090) and GABI_324A03 (At5g38420). The 1a3b mutant (GABI_608F01 (At1g67090); SALK_117835 (At5g38410)) was provided by Hiroyuki Ishida, Department of Applied Plant Science, Tohoku University, Japan.

Information as a critical

These same leaves exhibited a reactivation of photosynthesis in spring,

In the present study, the levels of photosynthetic down-regulation as well as the engagement and nature of the two different dissipation processes are examined in bearberry, which is a species that occurs over a wide range of conditions.

How does bearberry cope with this wide range of environmental conditions, coupled with high levels of solar radiation?

My Open Textbook: Pedagogy and Practice

Enabling scientific discussion on eLife with Hypothesis

Python filter support for Pandoc: on a Windows command prompt, type pip install pandocfilters

However, we have not had conclusive evidence that releasing these volatile compounds increased the fitness of the plant in the Darwinian sense of increasing reproductive success.

Manduca sexta,

Annotating

H5P as a Service coming Q1 2018

Bookdown site

Moreover, the class' Hypothesis activities were synced into a dedicated Slack channel named "Hypo Feed" via the Hypothesis' API; as such, social annotations containing the course hashtag (made by both formal or open participants) were notified on Slack as well, and Slack participants could react to a Hypothesis annotation by following a link provided in the notification (Goals 2, 3 & 4). 

Pink Squirrel Nymph

Cable Tie Craw

Mop 'N Glo 2.0

Dumb Bunny Streamer

for

However, these faculty members are also of the opinion that it is very time-consuming to teach these skills

scientific argumentation model (SAM), a heuristic consisting of a set of seven moves (unpublished data) that play an important role in an author's argument as given in research articles.

We report results from randomized, placebo-controlled, double-blind trials of antibiotic therapy inseropositive and seronegative patients who had chron-ic symptoms after treatment for Lyme disease.

it is important to determine the efficacy of suchtherapy.

In view of thesubstantial morbidity and even death5 associated withprolonged parenteral antibiotic treatment of Lyme dis-ease

We hypothesized that introductory textbooks under-represent the processes of scientific investigation and discovery.

Duncan (16) found that less than 5% of the figures in a typical textbook contain data. It is no wonder that students using a traditional and passive textbook do not know how to support their answers with data.

However, if reading the book is a key component of class time and tests, students will use the text to help them construct their own understanding of the material.

Second, students must come to class prepared for classroom activities, which also facilitates studying for exams as the semester progresses.

First, student work outside of class needs to be intentionally and effectively structured.

Our results also discourage modelsof guidance by default that involve repulsive guidance cuesfrom non-target cells, which has been shown to play a signifi-cant role in neural path finding (Dodd and Schuchardt, 1995).

Whatever the details of molecular basis of theguidance process is, there are two ways by which the femalegametophyte may accomplish this. (1) The gametophyte maydirectly change the surface characteristics of the epidermalcells lining the ovule stalk and the outer integument byproducing a surface-localized signal (Fig. 6B). (2) An alter-native mechanism would be, a signal from the gametophyteindirectly causing changes in the surface properties of thesporophytic cells along which the pollen tube tracks (Fig. 6C).This latter model demands that the primary gametophyticsignal is passed from the adjacent sporophytic cells to furtherneighboring sporophytic cells by the same or a differentsignaling mechanism.

A support for the second model (Fig. 6C) comes from theobservation that the abnormal ovules of the inner-no-outer(ino)mutants are defective in the final stages of pollen tube guidance(Baker et al., 1997).

These results convincingly demon-strate that pollen tube guidance by an ovule requires a func-tional female gametophyte, and excludes the model presentedin Fig. 1B

The resultsreported here allow us to conclusively reject the possibilitythata group of sporophytic cells of the ovule are responsiblefor guiding the pollen tube as well as controlling the femalegametophyte development.

The results are sum-marized in Table 4. Of the 184 morphologically normal ovulesscored, 124 ovules were associated with a pollen tube at themicropylar end. By contrast, none of the 189 ovules without anormal female gametophyte had a pollen tube guided to themicropylar end. The morphology of 137 ovules could not beunambiguously scored in these flowers because these wereeither squashed too hard or were occluded by the surroundingopaque tissues; however, approximately half of these had somepollen tube association.

MATERIALS AND METHODS

Therefore, at least the finalphase of pollen tube guidance to the ovule is controlled by thefemale gametophyte.

In this communication, we describe an explicit genetic testthat distinguishes between the above two models.

The above results forced us to entertain two alternativemodels (Fig. 1) that could not be distinguished in the previousstudy. One model proposes that the gametophyte produces asignal that directly, or indirectly through its effects on sporo-phytic cells, causes pollen tube guidance to the ovule (Fig. 1A).

In this study, we identified an earlier adhesion event thatallows plants to capture appropriate pollen.

To investigate the nature and role of cell adhesion in plants,we analyzed the initial step of pollination in Arabidopsis: thebinding of pollen grains to female stigma cells.

Pollen-stigma adhesion in Arabidopsis: a species-specific interactionmediated by lipophilic molecules in the pollen exine

“You might be able to get more lycopene out because the heat starts to break down the cell matrix and that actually allows some of the tied-up carotenoids to be released from the cell walls,”

We hope to integrate these themes and styles into bookdown, so authors do not have to dive into the details of how to use a certain LaTeX class or how to configure CSS for HTML output.

80/20

Can readers interact with examples in our book as they read it?

certain figures float to a random page,

his work led to the recognition that most enzymes are in fact proteins and in 1946 Sumner was awarded the Nobel Prize in Chemistry.

3,000-fold concentration differences between varieties

tomato flavor now seems to be a cherished ‘lost virtue’ of a recent but bygone era.

Course Structure

FIGURE 1.

, instructors have detected that students struggle with some of its aspects

In their report Scientific Foundations for Future Physicians, the American Association of Medical Colleges and Howard Hughes Medical (AAMC-HHMI) Institute listed the ability of critical reading and evaluation of scientific papers as one of the competencies that students should possess before entering medical school (AAMC-HHMI, 2009, p. 26).

8-10 quanta

In fact the photosynthetic rate achieved with the two light qualities combined could be 30–40% higher than the sum of the rates in far-red or shorter red when measured separately (Emerson et al. 1957).

Chl a/b ratios commonly range from 3.3 to 4.2 in well-nourished sun-adapted species, but can be as low as 2.2 or thereabouts in shade-adapted species grown at low light.

biochemical aspects of photosynthetic carbon reduction (Calvin cycle) are now comprehensively understood. The transduction of light energy into chemical potential energy is not so well understood, while events surrounding photosynthetic electron flow are defined in some detail and are described here, biophysical processes within the water-splitting apparatus of chloroplasts, and indeed the manner in which photons are captured and their quantum energy harnessed for photolysis, remain something of an enigma and fall outside the scope of our present account.

Photosynthetic capacity of leaves varies widely according to light, water and nutrient availability and these differences in capacity usually reflect Rubisco content.

. In part, this gentle transition reflects the fact that a leaf is a population of chloroplasts which have different photosynthetic properties depending on their position within that leaf.

For most leaves, 80–85% of 400–700 nm light is absorbed and it is only in leaves produced under severe nitrogen deficiency where there is less than 0.25 mmol Chl m–2 that absorptance falls below 75%. 

Expressed in terms of absorbed quanta, sun and shade leaves have virtually identical quantum efficiencies for CO2 assimilation. 

Section 1.1 encompasses anatomy, light interception and leaf gas exchange and includes a case study on development of a process-based model for photosynthetic CO2 assimilation using A:Ci curves.

variation

concept of function

m. In effect, we need to know collective behaviour (e.g. PV = nRT) before we can ask pertinent questions about the parts (e.g. how can we best summarise the behaviour of a legion of elastically colliding molecules).

rare exceptions

Osmond and Chow 1988

Accountability, philosophy and plant physiology

A plant science manifesto

satellite DNA

2.1.2 Levels of compaction

spool

tightly DNA is packaged

compaction makes it easier to transport DNA within a dividing cell, it also makes DNA less accessible for other cellular functions such as DNA synthesis and transcription. 

Knowledge of these hereditary properties has been of significant value in the history of human development.

Genetics

very hard to quantify that datum

marginalia

synthesis mapping,

As CO2 molecules diffuse inwards they encounter an opposite flux of H2O molecules rushing outwards that is three to four orders of magnitude stronge

cuticle

The lower half of a leaf absorbs about 25% of incoming light, but is responsible for about 31% of a leaf’s total CO2 assimilation.

Overall, absorption of visible light by mesophyll tissue is complex due to sieve-effects and scattering

weak absorption around 550 nm, which corresponds to green light.

of sections cut parallel to the leaf surface are shown for palisade

A thicker leaf in sunny environments is energy effective because enough photons reach chloroplasts in lower cell layers to keep their Rubisco gainfully employed.