Loving microbes

I thought I would write a post for all the non-microbiologists that might be wondering what microbes are in our logo and why.
Before that though, maybe I need to mention that there are a small number of bacterial basic shapes and the rest are just types of those basic shapes. Bacilli are rods, cocci are spheres, spirochetes are spirals, filamentous bacteria form long filaments that look like fungi, and pleomorphic are weirdos that don't adhere to one shape. In general (except for pleomorphic) when a bacterium is healthy and it divides, the two resulting bacteria look exactly the same shape (rod to rod).

Okay, so here is a vector version of the linocut logo I made:

So what are they?
 #1: A general bacterial shape called a vibrio which is just a curved rod. (The straight version is called a rod or a bacillus). An example of bacteria with this shape is Vibrio cholerae the causative agent of cholera.

#2: This is a chain of the bacterial shape called cocci. The kind of cocci that form a chain like this are from the genera Streptococcus, Lactococcus, and Enterococcus. Lactococcus and Enterococcus were classed as Streptococcus until 1984 and they are difficult to distinguish from streptococci by morphology alone (shape). All 3 genera are found living in and on humans. Most are either beneficial or neutral, while some can be pathogens. (Genera is the plural form of the word genus, and is the classification level above species - wikipedia explanation here - scroll down to Modern system of classification for a good graphical explanation).

#3: This is a bunch or cluster of cocci and the kind of cocci that form this shape are from the genus Staphylococcus. Staph are also found living on and inside of humans and some are neutral and some are pathogens. The most famous of the pathogens at the moment is Staphylococcus aureus because it is increasingly methicillin resistant (MRSA) making it very difficult to treat.

#4: This is my poor representation of a spirochete or a really twisted vibrio. I didn't have any particular bacteria in mind for this shape but well known spirochetes are the Treponema which cause syphilis and the Borrelia which cause Lyme disease.

#5: This is a bacilli with fimbriae which is common among Escherichia coli that cause urinary infections. The hairy-like fimbriae help the bacteria to attach to the host cells.

#6: 6a and 6b are different serotypes of the same species of bacteria. Streptococcus pneumoniae (or the pneumococcus) exists as diplococci (doublets) instead of chains like other streptococci. It can have a sugar capsule (b) to protect it from the immune system or not (a). Pneumococci without capsules are generally not pathogenic. Pneumococcus lives in humans mouth, throat, and nasopharynx and can sometimes cause disease. I included both forms because I have studied the pneumococcus for many years and it is a bacterium near and dear to me.

#7: This is a bacilli with flagella. A flagellum is larger and longer than fimbriae or pili and is used for movement rather than attachment. Pseudomonas is a genera of bacilli bacteria that have flagella. Another famous bacteria that has flagella is Helicobacter pylori - generally H. pylori are considered vibrio (curved rod) but in some pictures the curvature looks small and it looks like a normal bacillus).

#8: Neisseriae or coffee-bean shape in pairs is also another cocci bacteria. This shape is particular to the genus Neisseria. There are 11 species of Neisseria that colonize (live in/on) humans and only 2 are pathogens. They are Neisseria meningitidis (causes meningitis) and Neisseria gonorrhoeae (causes gonorrhoea).

#9: Similar to #7 but I was specifically thinking of Salmonella and more specifically Salmonella enterica. Various strains cause typhoid fever or food poisoning.

#10: Depending on my artistic skills and your interpretation these can either be tennis racket or drumstick shape common to Clostridium tetani, the causative agent of tetanus, or the clubbed rods of Corynebacterium diphtheria which cause diphtheria.

Some of the shapes I played with the sizes - so these sizes are not to scale! For example, the staph, strep, and pneumos should all be about the same size but the pneumos look much bigger here. I included shapes I either thought were interesting, or important bacteria, or bacteria that I am personally interested in (like streptococci). One major bacteria I didn't include is the basic bacillus shape common to Bacillus anthracis (anthrax) and Mycobacterium tuberculosis. It just didn't look good to me so it was omitted.

And there you have it- a crash course on bacterial shapes.

Paper

There are many things that matter when printmaking, even more so when doing everything by hand (IMO), but I have come to the conclusion that the paper you use might matter more than others. The texture of the paper, the color, whether it's hand- or machine-made, whether it has inclusions or areas of variability all effect the print. These aspects of paper effect how the print looks in an aesthetic way, but also in a practical way. The way the paper soaks up the ink (or not), how easy it is to hand burnish (or not) can have a huge effect on the resulting print. Some papers have caused me to tear my hair out, convinced I was a horrible printmaker and ready to give up completely.  Similarly, finding the "right" paper for a piece can be a revelation.

I have had a formal visual arts education, but printmaking was never offered at the uni's I went to, so all of what I now know (and am still learning) about paper in printmaking is pretty much trial and error. Some of it I have gleaned from blog posts of other artists, or descriptions on art supply websites, but I found that opinions on paper can vary vastly depending on the printmaking equipment you have at hand. The paper that works for people using a press is probably not suited for hand burnishing. Since I don't have a press, I can only comment on hand printing techniques.

Something to keep in mind that I'll cover in future posts is the type of lino you use and the type of ink roller can also effect the way the print appears on the paper. So it's not all about the paper, just mostly. To be brief, I mostly work with vinyl and a soft esdee ink roller.

Okay, enough of the generalities, lets get into some details.

I do a test print on regular white printer paper. If I like the design of the lino and I want a digital image I'll make a good print on this kind of paper since it photographs really well. I could probably use newsprint, but that would require me to buy something extra, so I haven't switched yet.

After the test print I'll do a first round of proofing on off-white 100 gsm artist sketch paper (cartridge paper). Since it's off white and has a slight tooth to it, it gives me a good idea of what the print will look like on most of the other papers I use.

The first artist "printmaking" paper I bought and tried was Hahnemühle Ingres 100 gsm watercolor paper. At the time we were living in Netherlands and I was getting my supplies from Gerstaeker, a really great supply company (more on them later), so I trusted their paper recommendation. This is one of the papers that caused me to tear my hair out. Usually paper sticks to the ink on the lino and you can burnish away but this paper doesn't and the image gets all distorted. It only works if you stamp it - ie place the lino on top. And even then, the cross-hatch raised pattern of the paper shows through unless you have way too much ink. It might work in a press. I'm not sure. Just for shits and giggles I tried it again recently - here's the result.

 Double image from paper moving during burnishing.

 

Poor ink uptake if you just press on the paper with a book and your own bodyweight. Plus you can see the paper pattern through the image.












The next paper I tried can only be bought in the USA (so far as I can tell). The company is called Black Ink and the paper is Block printing Kozo sheets. The weight is 45 gsm. I got mine at Dick Blick (link here). I really like this paper. It's great to work with for hand burnishing. The limitations are that it only comes in one size (9 x 12 inches) and I cannot, for the life of me, find it here in the UK. I have a few sheets squirrelled away for print editions already started.

And thus started my quest to fins something similar in the UK that I could get in a bigger size.

I found a kozo at the online supplier AtlantisArt in several weights. It's Khadi Mulberry tissue paper, and I tried the 30 and 25 gsm papers. This paper was not like the other brand of kozo. This paper is very, well, fluffy. It's not like the kind of tissue paper I think of, it's more like actual kleenex. I did one edition of ten prints on the 30 gsm (Etsy link), and I like the results, but, I wont be using it again. It's very difficult to cut, tears easily, difficult to write on it, and it leaves tiny fibers all over the lino every time you print, so I ended up cleaning the lino in between each print. Very tedious. It was also prone to tearing while I was burnishing, so I had to place a piece of printer paper between this paper and my barren.
Here's the print:

Then I found various other thin papers, lokta, kozo, shoji, masa, etc. I decided that instead of using each one with different inks and linos to just do a trial print run on every paper with the same lino and ink on the same day to compare the results. And I'm so glad I did!

I'll go through each paper. I actually like many of them, but not all will work for every print.

First is the Japanese Masa. It only comes in bright white. I got it at Intaglio Printmaker online (link). It is 86 gsm, and a generous 790 x 530 mm (31 x 20.8 in) per sheet. One side is smooth with a slight sheen to it, while the other side is a bit rough. On the rough side you can see the laid lines. This paper is machine made and quite uniform. I printed on both sides and like the smooth side better. It is very easy to hand burnish and produces lovely bold outlines and details. You can really get good ink saturation with this paper.

Second, is a paper very similar. It's Japanese Shoji made of Kozo. It's also from Intaglio Printmaker (link), and also bright white. It's a thinner 45 gsm, and still a generous 960 x 620 mm. Also like Masa it has a smooth side and a rough side, with barely visible fibers on the rough side. I only printed on the smooth side. The feel of the paper is slightly nicer than the Masa, in a way hard to describe. Hand burnishing was very easy, and the print has good outlines and details. The colors aren't as saturated and bright as the on the Masa, but this was my favorite paper for this particular lino/color combination.

Next was Japanese Kozo paper, from Intaglio Printmaker (link). They sell both white and natural and I chose to buy the natural. I'm a bit annoyed that they don't supply the information on the weight, just call it "lightweight." My guestimate is 25 gsm. The smooth side has less of a shiny sheen than the Masa and Shoji, and the rough side is a bit less rough as well. Laid lines are visible on the rough side. The paper is machine made, but does have some areas of variability and visible fibers that give it character. It prints nicely and is easy to hand burnish. This is the closest match to the Black Ink Kozo paper. The colors don't print as saturated, but that might be because of the natural color and not because of the paper. I like it a lot, but just not for this particular print. But I will be using it for other prints.

I also bought Fabriano Unica and Rossapina (from Intaglio Printmaker) to try but realized when they arrived that I would probably have difficulty hand-burnishing these papers so I'm saving them for some other purpose.

 Next I printed on Khadi Nepalese Mitsumata Washi paper from Atlantis Art (link). This is a 30 gsm handmade paper and it is just gorgeous. It didn't work with the image I was going for for this particular print, but I will be using it again in the future. It is 760 x 560 mm (30 x 22 in). Like the other papers it has a smooth side and a rough side. It is a lovely creamy color, like aged books. However, even on the smooth side, there are bits of inclusions that interrupt the print (you can see them in the picture below where the blue ink seems to hit a speedbump. This is not necessarily a con, it would just need to go with the linocut design.

The next paper was by far the darkest paper I tried. It is Khadi Mountain Lokta paper from Atlantis Art (link). This paper is also handmade and 30 gsm. The size is 750 x 500 mm. The color is like a dark antique bookpage, maybe stained by tea. The smooth side of this paper is not as smooth as the Mitsumata and no where near as smooth as the Shoji or Masa. You can see a slight honeycomb pattern on the smooth side and the ink didn't take as well on this paper. It also moved a bit while burnishing. It's no where near as bad as the Ingres, but something to keep in mind. There are very obvious fibers visible and lots of inclusions and areas of varying paper thickness. I still haven't decided if I will use it for printmaking in the future.

The next paper was a Lokta paper from Cass Art in Birmingham. There wasn't any information at the store other than it being Lokta, but if it's the same product online then its by RK Burt and 65 gsm. It's a creamy color and a softer paper, close in feel to the Khadi kozo. It is also difficult to cut, but doesn't leave a mess in the lino after printing. It doesn't stick to the lino as well as the other papers, and in some areas I double printed the image while hand burnishing. Since it is so soft, I put a piece of printer paper on top so that the force of burnishing wouldn't destroy the paper. I think it might be suitable for small prints or stamping, where weight is applied to transfer the ink as opposed to rubbing.

The last paper I tested was the biggest surprise. It's a very lovely paper, but I thought no way will it print nicely by hand, but I tried it anyway just to see (for science). It's Khadi Rag & Fibre Paper - Smooth Banana. Another handmade gem by Khadi and supplied by Atlantis Art (link). It's 210 gsm and 760-560 mm. This paper had the most variability in quality at the edges than all of the other Khadi paper I tested and I ended up cutting some of the ends off as they were a bit worse for wear. Which kinda annoys me as I don't like wasting paper, but it is handmade. It's made from cotton rag and banana fibers and I would call it speckled. The base is a cream color, but there are a lot of inclusions of various colors that give it a lot of character. Even though it's called smooth, it is quite textured on both sides. This is very obvious in the blue section of the print. But, I actually like this effect. Since I thought no way would this stick to the lino, I decided against burnishing and put a large book on top and all my bodyweight I could muster. It worked fairly well, actually. The black part of the cat came out perfectly - saturated color, nice detail, good outlines. I'm guessing that this is what it's like to use a printing press or a nipping press - you can use thicker paper that has some texture and still get a good crisp print. I'm sure I will find a print to do on it in the future, it may just be small as it required quite a lot of effort on my part to press my body on the book for the print.

And there you have it! A tour of paper! There are other papers I use for printing bookmarks and cards, but they are (mostly) not fine art papers and so I will cover them in a different post. There is one paper I didn't cover, and that is Hahnemühle Green Rooster bamboo and cotton paper, but I have a lot to say about it, so it would make this post too long.

Back

Hey, hi, I'm back. It's been a long time since my last blog-post. In case that you don't follow @LoveBacteriaArt on the Twitter, the reason that I let the blog wither had a bit to do with life being overwhelming for so long. We were barely managing to keep the Etsy shop open. Moving country, starting a post-doctoral research position, husband getting cancer (and subsequent treatment), PIL's cancer coming back, and my migraines made quite the toxic combination. My job contract ended in June, and I am currently job hunting, but also working on my art and the Etsy and Redbubble shops. So I decided it was time to resurrect the blog.

So look forward to posts on all sorts of things - art, science, bacteria, SciComm, SciArt, printmaking, and possibly cat pictures. Because the internet runs on cats!

So stay tuned!

Gift Books!

Received some very cool books this year for Christmas from my lovely partner.

I have not yet reached the part of the first book where it describes how to cure the plague, but I have read some very interesting cures for toothaches, warts, and genital diseases. Not surprisingly, many of the "cures" include bloodletting, poisonous substances (like mercury!), and/or opium. Don't worry, this book is for purely entertainment purposes! 

Anatomical planes of orientation

Right so I meant to write this post earlier but then packing and organizing and cooking dinner got in the way. So here we are, it's almost midnight on Christmas Eve.

It's important to mention the anatomical planes so that when I describe how I make the "Slice" series of linocuts everyone understands the vocabulary I use.

Almost every creature is divided by scientists into directional planes. This is so that everyone can communicate about the anatomy of various creatures. Some of the words used are the same or similar for many different organisms, which can help scientists, anatomists, dr's, whoever, to find analogous structures in different creatures (this is especially useful in evolutionary biology where you compare the structure and function of various body parts to understand how life has formed over eons). For the most part, the planes of the bodies of mammals are the same words. This is makes anatomy and research using non-human animals easier to compare to humans. Ok, on to the planes themselves.

The easiest way to understand planes is to imagine that a giant guillotine is making a slice (this is in essence what anatomical dissections do, and why we need these words). So the coronal plane, which divides the body into ventral and dorsal (belly and back) sections would be a blade slicing through the skull parallel to the eyes. (It may help to look at the awesome wikipedia for illustrations). The sagittal plane is perpendicular to the coronal plane. It separates the body into right and left sections. Imagine a blade slicing through your nose, perpendicular to your eyes. These are the two most important planes for now.

To recap: coronal sections would slice with the blade parallel to the eyes, so in essence would slice the tip of the nose first (on a human), then the nose off, then the forehead and lips, etc. These kinds of sections would give details on the structures from front to back in a skull (where they are, where they are in relation to other structures, size, and what they look like etc). Sagittal sections would first slice off an ear, then one side of the whole head perpendicular to the eyes. These kinds of sections would give information on the different halves of a skull, and what particular features look like going from right to left or from outside to inside.

Hmm, I hope this makes sense. May edit in the future with some illustrations.

Nearing Christmas

Frank Sinatra Christmas is on Spotify, the cat is exhausted and sleeping under some packing paper, I packed Some boxes (ok, 2), and I'm sipping some mulled cider (the non-alcoholic kind). If only I wasn't in Utrecht with the cat and the boyfriend in England with his family. But anyway, is there anything better than Frankie's rendition of "Let It Snow"?? No. There is not. My mom would argue that Bing Crosby is way better, but this isnt her blog. (:

T-minus 1 day until the Etsy shop goes in vacay mode for our move. I'm actually more nervous about this than I was for opening the shop. What if someone wants to buy something and cannot? Well, I hope they check the blog and can wait until January!

For those of you traveling, stay safe and good luck!

Next post will be more science, and maybe, finally, some art!

Histology

Right, so I promised a post on histology and then a migraine happened. And migraines don't give a sh*t about what you have planned to do. Things are increasingly hectic here as we get down to the 2 weeks left to move mark, and still no idea of how the actual move is going to happen (long story short the guy we hired to move us has health issues and my driver's license could not be renewed).

So, histology. What is it? How is it done? Why am I talking about it?

What is it???  Histology is the study of anatomy under the microscope. It's micro-anatomy! For reference, gross anatomy refers to the study of large structures that you can see by eye, not disgusting anatomy. The sister of histology is histopathology, the study of disease anatomy under the microscope. Scientists who study histopathology also study histology, because you need to understand what the structure looked like before the disease occurred. Histology can encompass anatomy of anything that can be seen under a microscope, human specimens, animal, plant, fungi, you get the idea. Usually specimens are sliced very, very thin, then stained with special dyes to aid the viewer.

How is it done???  First, you need to decide what you want to study. Often you choose an area or an organ or a tissue specimen. The specimen then needs to be removed and extraneous material removed (sort of like cleaning). An easy thing to study would be the structure of an organ like the spleen or liver, as these are easy to identify, remove, and prepare (they are soft). A difficult thing to study would be bone, and a really difficult thing to study is an entire area like the arm or the upper respiratory tract (where you breathe - from your nose to the sinuses). If the thing you want to study is soft, like an organ, you only have to put it in fixitive and wait. Fixatives like formalin (a derivative of formaldehyde) preserve the specimen. If you want to study something that is not soft, then (usually) you must make it soft after you fix it. If you are working with bones or cartilage, you can soak it in EDTA which is a chelating agent and decalcifies the bone. Next the specimen gets filled, or embedded with a stable compound like paraffin that will keep the structure. Formalin-fixed paraffin-embedded (FFPE) tissues have the added bonus of being stable at room temperature for decades. Possibly even centuries.
          ** Side note - the stability of FFPE specimens allows scientists to do some pretty awesome things like go to biobanks, look up specimens from say, the 1918 influenza pandemic, and make fresh samples to study with modern methods, greatly increasing our knowledge of the past. -- This in turn can inform our future. Big universities or government science facilities that store banked specimens are a huge treasure trove of new possible discoveries, or re-discovories.

Once the specimens are embedded, they are sliced until a proper depth is reached. A 'proper depth' can mean just about anything, depending on what the scientist wants to see. Once at the right area/depth, very thin slices (2-5 um) will be taken and mounted onto glass slides. This is why the tissue needs to be "soft." In order to get a thin slice that does not damage the structure, the blade must move through like butter. The blades are very sharp, but things like hard bone would still destroy the blade and the specimen.

After it is mounted onto a glass slide, the paraffin is removed, leaving just the tissue or specimen. Then a variety of stains can be used that highlight various structures. One of the most common stains in the study of anatomy is called H&E (hematoxylin and eosin). H&E are a stain and a counterstain, and depending on the structure you will see a variety of pink, deep pink, or purple colors. The nucleus of cells stains a rich purple, whereas the cytoplasm generally stains pink.

Here are some examples of H&E stained samples (pictures I took myself!). Click on the picture to enlarge it.

This is a section of a mouse lung that had a bacterial infection.

 This is a mouse lymph node, similar to the tonsils

This is a mouse sinus cavity, complete with phagocytic macrophages **EDIT I'm pretty sure it's a blood vessel inside the sinus area. (I'm not an expert)













A lot can be learned from histology, not just anatomy. This is why scientists still today use histology and histopathology, which are basically techniques first introduced over 100 years ago. Now we have some new and cool stains that can tell us more about the function of certain things, but the basics are roughly the same.

And finally - why am I talking about histology??? I am talking about it because it forms the basis of the "images" I use in my art. In my life as a scientist as I use histology and microscopes quite a bit. Because I think that what I see under the microscope is wondrous and beautiful, I decided to create art prints based off of this. Linocut printmaking is an analogous process in which you must make fine, deliberate cuts, and then add ink to reveal the final piece. This is part of the reason I chose the technique. I think it gives the same feeling as a histological picture.

So, I hope everyone has enjoyed my crash course in histology.