Spider Eyes are Nature’s Marvels

Now I do not exactly remember where and how I started my journey down this rabbit hole. But the deeper I went the more interesting it became. It was a great learning experience. I’m clearly not an expert. Here I share the understanding I developed of the spider eye over the few hours of exploration. For this I referred to various sources all of which are mentioned in the links. And if you know more or would like to add something interesting to the article please let me know in the comments below.

The  first thing about spider eyes is that 99% of spiders have 8 eyes. A little less than 1% of them have 6 eyes. In some fringe species there are 4, 2 or no eyes at all. Apparently, based on the pattern these eyes are arranged in, on their cephalothorax (let us mortals call it the ‘head’ to make things simple), the family to which the spider belongs can be determined. Some blessed human, made the following schematic to help us do exactly that. In case you ever feel the need to do so, here it is:

And in much greater detail, right here.

For their small size and the limited number of photocells, spider eyes, especially the jumping spider’s (Salticids) eyes perform surprisingly well. Their resolution is better compared with larger mammals than with insects. In the human world a camera of such standards this would simply be an engineering miracle. You will understand why I say that soon…

In the image above if you locate the family Salticidae, you will see those two large eye in the front which are particularly very interesting. These are called the principal eyes (or anterior median eyes) and are the ones that allow high resolution vision. So much that the spider would be able to resolve two spots on a screen 20 cm away from the spider, sitting just 0.12 mm apart from each other. An acuity of about ten times that of a dragonfly – 0.04°.

The brain of this spider, show in blue in the image below is pretty big for its size. The proportion of the volume of brain to body is more or less similar to that of human beings. The brain of Salticids also have a rather large region dedicated for visual processing.

The principal eyes we are talking about are in the shape of elongated tubes as seen below, in the front of which is a hard lens and at the other end is a layer of photocells. Inside the tube, near the retina is another little lens which moves back and forth along the tube like a telephoto lens system. These elongated tubes are like the tubes of a binocular which allow for a higher resolution using a small package.

However the downside of such a tube like architecture is that it limits the field of vision. Here’s how that problem is dealt with.

The front part, with the big corneal lens is fixed. It has a long fixed focal length. The farther end where the retina is located, is connected to these muscles shown in red. These muscles allow for the tube’s farther end to move around in several degrees of freedom to make quick movements and scan a larger image in its head, one small field of view at a time.

In the video below you can see the retinal end of the black tubes moving around inside the translucent exoskeleton of the spider as the spider forms a high resolution complete image of its surroundings, one small field of view at a time.

If you peer deep into their eyes you will see a dark (black) when you are looking into the small retina. However when the farther end of the tube moves, you see a honey brown color with spots. This is the inner wall of the tube that you are seeing in the following video.

Then the retina itself is another biological marvel. Unlike our single layered retina, the Salticid’s retina is made up of four layers. The four layers are arranged one behind the other. This lets the nature pack more photocells in a smaller area and also helps the spider see in color as different colors (different wavelengths) with different refractive indices are focused in different planes.

Counting from the rear end, the spider uses different layers of retina to obtain different colors of the image. The retina’s layer 1 and 2 to get the green color (~580 nm – 520 nm wavelengths), blue color using the layer 3 (~480 – 500 nm wavelengths) and layer 4 for ultraviolet (~360 nm).

An important detail in the above image reveals how spiders manage to keep focus on different objects at different depths, in focus. The layer one has photocells arranged in a step fashion, with varying distance from the lens which makes sure that all objects are focused on at least one part of the layer 1.

The other problem of distance estimation which matters a lot for jumping spiders is again solved rather elegantly by the same apparatus. Humans use their stereo vision – two eyes which are far apart to estimate distance. Other animals move heads to do the same but I’m not getting into that.

Jumping spiders employ a completely different algorithm, utilizing degree of blur cues. For which the second layer plays a crucial role. The second layer would have received a sharp blue image, but they are not sensitive to blue light like I mentioned above. The green they detect is rather blurred at that plane. It turns out that the amount of blur depends on the distance of the object and helps the spider determine the depth by processing the amount of blur in the image. Hence allowing it to jump and hunt accurately.

If you are a university student with free access to journals, I think a quick look at the paper titled: “‘Eight-legged cats’ and how they see – a review of recent research on jumping spiders,” will help you delve into greater detail.

Psst: Someone has it uploaded on research gate for free access for I don’t know how long: here.

Please leave a comment below to let me know your thoughts on this, or if you have any ideas for future posts. I plan to reward the top commentators every month so do not forget to say something.

Frozen Tissue Array Methodology, Applications and Benefits

Frozen tissue array is a methodology that is used in modern molecular and clinical research to analyze hundreds of tumor samples on a single slide. It allows a high throughput analysis of proteins and genes in a huge unit. It consists of frozen tissues where separate tissue cores are lumped together to allow simultaneous histological analysis. It has made it easy to streamline several research projects thus saving significant time. It also conserves precious reagents for analysis numerous slides that contain a single section per slide. It is an ideal screening tool that is used before

embarking on extensive research and analysis.

Preparation of frozen tissue array

Each product is produced using the state-of-the-art preparation technique by the use of the finest quality specimens. Upon excision, the tissues are then placed in liquid nitrogen and then sorted meticulously by an expert pathologist. Cores from 20 different tissues or more or with pathologically relevant tumors are then combined in a single block. With the use of unique staining methods, the quality of each
slide is selected. Tissues with a diameter of 2 mm from the region of interest
are sorted from frozen tissue OCT blocks by varying their freezing temperatures, see more here.

Features of frozen tissue array

Every product is designed to conform to the FDA guidelines and must meet the requirements of therapeutic antibody validation and vitro diagnostic device certification. There is a vast range of tissues in every array. The technique is suitable for both radioactive and non-radioactive detection. It combines arrays from variety human donors. Compared to paraffin-embedded tissues, frozen array tissue contains better antigen exposure.

Frozen Tissue array applications

The technique has been employed in various areas such:

  • Rapid screening of protein expression or novel gene against a large panel of tissues
  • Diagnostic and high throughput therapeutic analysis in antibody
    variations
  • Analysis of gene expression patterns
  • In situ hybridization and used together with immunohistochemistry
  • Novel gene and protein expression comparison
  • It is also an excellent approach in FISH-based experiments in the
    analysis of DNA. In summary, frozen tissue array provides an excellent target
    material for an effective study of RNA, DNA, and proteins.

Samples of DNA, RNA, and certain antibodies don’t perform optimally when used in pre-fixed paraffin-embedded tissues. However, they work pretty well when used in frozen tissue array. Again, the procedures that require fixation can be identified and conducted in an appropriate manner. This means it is possible for you to include a wide array of samples in your final analysis than when using the paraffin-embedded
procedure
The only drawback with frozen tissue array is that some cell morphology and tissue architecture distortion is likely to occur. This can be seen by comparing it with the sections from paraffin-embedded. Additionally, a limited number of samples can be embedded in one array. This is due to the fact that there may be a tendency of OCT compound cracking or bending particularly when samples are placed one millimeter apart.

Conclusion 

The invention of this technique has become a boon to many scientists from around the world. It has saved scientists and pathologists significant time when conducting several tests. It also has numerous potential applications in basic research,
prognostic oncology, and drug discovery.

Determining methods of Automated Nucleic Acid Extraction

By Lorenzo Gutierrez

Scientific exploration- Determining methods of Automated
Nucleic Acid Extraction

The human body is a complex structure made up of various cells and genes. The central system of genetic identification for humans is focused on one’s DNA, that is deoxyribonucleic acid. It is present in nearly all living organisms as it defined as the main constituent of chromosomes. With the introduction of a variety of communicable diseases, it is pertinent to researches to be able to extract DNA. They do this to run various tests to see how best the world’s population can extend its life cycle through science.

What is Automated Nucleic Acid Extraction?
This speaks to the removal of DNA by mechanical/ automated means. Extraction by this mean is deemed to be more accurate and more beneficial to science as it lessens the margin of error, or so it is alleged. “Automated nucleic acid extraction systems can improve workflow and decrease variability in the clinical laboratory.”[1]There are various methods that can be accessed. As science evolves so does technology and technological research is by extension advanced.

Methods of Automated Nucleic Acid Extraction
There are various methods of extraction and various machinery used by researchers on a day to day basis in efforts to attain much needed samples of DNA. This is done as the fight towards cures for many communicable diseases is a rather tedious process. Let us face the fact that technology is put in place to lighten the work load of many and aid in movements towards more accurate results. Many companies have delved into the creation of different extractors that each operate at varied levels. Some of which were created to be work horses, thereby being able to complete massive amounts of work while others are able to only produce an average turn out. Laboratories vary by size and as such, they would be able to best choose an extractor of their liking to perform their work functions.

There is the manual means of extractions, you can refer to this as good old reliable. Researchers are incredibly consumed by work when they have to utilize manual extraction methodologies as it is incredibly hands on. Of course, there is the usage of some level of technology however, the researcher would need to be present to adjust variables and incorporate other items as the need arises.
Automated Extractors allow researchers the ability to set their research in the machines and be able to leave to complete other tasks. Researchers aren’t needed at every step during automated extractions as technology does most of the work once it is that the samples are prepared and placed therein. It must be noted that with the presence of great technology, companies also incur a greater cost. Where a manual extraction could be performed at approximately $5, the work of an automated extractor could range anywhere from $7.60 to $12.95 per sample.
You may find that, true to human nature, researchers will gravitate towards a more established extractor as it had been around longer and there had been numerous reports done on it. However, it is important to still venture out and try new machinery as prior to the one that is most renowned became that way it was merely extractor X for argument sake, an unknown machine with the potential to create an ease of workload.

Research of two methods [2] For the purposes of this article we will look at a particular research performed by a group of research scientists, their information will be provided below. After comparing the three methods of extraction, It could be determined that the first extractor; X was reasonably efficient as it varied from 86% to 107% of manual. The second extractor Y’s recovery efficiency in comparison to the manual method varied from 83%-107%. Though the results varied marginally the true variation of extraction came by way of cost. As the extractor X was the most costly means at $12.95 per sample, whilst the Y costed $7.60. There is also a key difference in operational actions as the X doesn’t allow for the researcher to walk away, leaving the machine to perform its extraction. The X also needs a higher volume of samples to perform its task. Automated Nucleic Extraction is a field of science that is beneficial to researchers as it yields greater results than manual extraction. It is however a more costly approach.

[1] Dundas N., Leos N.K., Mitui M., Revell P., Rogers B.B. (2008 June 13) Comparison of automated
nucleic acid extraction methods with manual extraction.

[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2438199/
Retrieved August 3, 2017