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Homogeneous and complex nuclei

Homogeneous and complex nuclei


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In the Wikipedia article on nuclei one reads:

"The neurons in one nucleus usually have roughly similar connections and functions."

I read this as "a nucleus usually is roughly homogenous", i.e. contains a small number of neuron types, distributed roughly equally and with a roughly homogenous connectivity pattern.

But it is also stated:

"A nucleus may itself have a complex internal structure, with multiple types of neurons arranged in clumps (subnuclei) or layers."

What I would like to know:

  1. Is my reading correct?

  2. Are there really more nuclei of the more simple (homogeneous) type than of the more complex type?

  3. Which are prototypical examples of both of the types (more simple and more complex)?

  4. Which are the greatest nuclei of "the" simple type (with respect to volume or number of neurons, taking "simple" with a grain of salt)?


  1. I think you are reading too much into that statement. The proper reading of that statement is to add on the implied "… compared to other nuclei." That is, what defines a nucleus, in most cases, is some shared similarity in connectivity. That does not mean homogeneity.

I also think your reading of the second statement is incorrect; it does not suggest that there are "simple and complex" nuclei as two distinct categories, rather it is indicating that "complexity" varies, and gives a couple examples; essentially, it is exactly saying that you should not assume homogeneity.

  1. I don't think it makes much sense to think in terms of "number" of nuclei, and anyways, nuclei can be somewhat arbitrary. For example, take the auditory thalamus: the medial geniculate nucleus (MGN). The MGN is typically divided into three parts: the dorsal, ventral, and medial divisions. Someone chose to call them all the medial geniculate nucleus, based on gross appearance, but with more functional understanding we can classify each part separately. Should this be one nucleus or three? It really doesn't matter, it's just semantics and terminology to get people talking about the same structure. In one context, it makes sense to talk about the whole MGN, in other cases it makes sense to differentiate between MGv, MGm, and MGd. You could call them subnuclei, or nuclei, or whatever you want. Most people choose to just be consistent with the terminology used in their field for historical reasons because it doesn't matter.

  2. I don't really think it makes sense to think of in terms of prototypes; nuclei are different from each other.

  3. Again, you'd have to first define simple and complex. I don't think there is meaningful dichotomous distinction.


Superior olivary complex

The superior olivary complex (SOC) or superior olive is a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. The SOC is intimately related to the trapezoid body: most of the cell groups of the SOC are dorsal (posterior in primates) to this axon bundle while a number of cell groups are embedded in the trapezoid body. Overall, the SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates.


The things that make a eukaryotic cell are a defined nucleus and other organelles. The nuclear envelope surrounds the nucleus and all of its contents. The nuclear envelope is a membrane similar to the cell membrane around the whole cell. There are pores and spaces for RNA and proteins to pass through while the nuclear envelope keeps all of the chromatin and nucleolus inside.

When the cell is in a resting state there is something called chromatin in the nucleus. Chromatin is made of DNA, RNA, and nuclear proteins. DNA and RNA are the nucleic acids inside of the cell. When the cell is going to divide, the chromatin becomes very compact. It condenses. When the chromatin comes together, you can see the chromosomes. You will also find the nucleolus inside of the nucleus. When you look through a microscope, it looks like a nucleus inside of the nucleus. It is made of RNA and protein. It does not have much DNA at all.


Xylem Parenchyma: Origin and Phylogeny | Complex Tissue

In this article we will discuss about:- 1. Origin of Xylem Parenchyma 2. Phylogeny of Ray Parenchyma 3. Phylogeny of Axial Parenchyma.

Origin of Xylem Parenchyma:

Xylem parenchymas cells are present both in primary and secondary xylem accordingly their origin also differs. In primary xylem they originate from procambium. In secondary xylem ray parenchyma cells originate from the ray initials of cambium. The fusiform initial of cambium gives rise to axial parenchyma along with tracheary element and fibres.

Fusiform initials of cambium normally divide vertically in the longitudinal plane. Transverse divisions do occasionally occur during the formation of additional initials, but these are much less frequent than vertical division. The vertical divisions are mainly periclinal.

In these cells anticlinal division also occur to keep pace with the growth of stem in girth. During longitudinal division cell wall first originates between the two newly formed nuclei and gradually extends towards the ends of cell. The cell wall formation may not be completed for some time after mitosis.

Phylogeny of Ray Parenchyma:

In radial longitudinal section it is observed that the ray parenchyma is composed of square (isodiametric), erect (upright or vertically elongate) and procumbent (radially elongate) cells. It is considered that the square cells are morphologically equivalent to erect cells. The ray cells may be homocellular and heterocellular.

The homocellular rays are composed either of square cells or of erect cells, or of procumbent cells, or of erect and square cells. The heterocellular rays consist of both square and procumbent cells or of erect and procumbent cells. Rays may be uniseriate when they are composed of one cell in width, biseriate (ray is two cells in width) or multiseriate where the rays consist of a portion more than two cells wide.

The latter may have uniseriate wing similar to uniseriate rays. Multiseriate ray, as seen in tangential longitudinal section (TLS), is tapered towards both upper and lower margins. Tapered ends are described as wings, which is commonly uniseriate. The outline of rays appears to be fusiform in TLS. Primitive and advanced wood exhibit the following types of rays.

Carlquist (1961) showed some trends of evolution of ray types in dicots based on the works of Kribs (1935) with modifications and recognized the following type of rays:

It consists of uniseriate ray and multiseriate ray with uniseriate wings. The cells of wings are more or less similar to the cells of uniseriate rays. Both rays are of marked vertical length, i.e. very high. The cells are square, erect and procumbent.

This type is composed of multiseriate rays with short height and short wings. The cells are square, erect and procumbent. This type also consists of uniseriate ray with square and erect cells.

The rays are uniseriate and the cells are square, erect and procumbent.

The rays are uniseriate and the cells are square, erect and procumbent.

The rays are uniseriate and multiseriate with very short wings. The multiseriate rays are mostly fusiform. The cells of multiseriate portion together may be oval, round or radially elongated in outline. The cells of the uniseriate tips are identical with the cells of multiseriate portions of rays. The cells are procumbent.

The rays are multiseriate with extremely short wings and the cells are procumbent. The shape of multiseriate rays is fusiform. The cells may be round or radially elongated.

This type consists of uniseriate rays with procumbent cells. Carlquist showed the trends of evolution of rays in dicots which is presented in Fig. 10.1 in diagrammatic figures.

Woods having heterogeneous I type of ray is considered as primitive. The advanced form of rays is either uniseriate or multiseriate with procumbent cells (Homogeneous I, II and III). It is regarded that the rays with erect cells increased in length and continued elongation resulted the conversion of ray initial into fusiform initial. The ultimate result is raylessness.

Phylogeny of Axial Parenchyma:

The fusiform initial of cambium gives rise to axial (vertical) parenchyma. The distributions of axial parenchyma are studied in transverse sections. Axial parenchyma may lie independent or associated with vessels. Accordingly timbers may be apotracheal (parenchyma are not associated with vessel) and paratracheal (parenchyma are distinctly associated with vessels).

The common apotracheal forms are:

(i) Diffuse (axial parenchyma occurs as isolated strand),

(ii) Diffuse-in-aggregates (axial parenchyma occurs as aggregates),

(iii) Banded (axial parenchyma appears as bands the bands may be narrow or wide),

(iv) Marginal [parenchyma occurs either at the beginning of growth ring (initial) or at the end of growth ring (terminal)].

The common paratracheal forms are:

(i) Scanty (the parenchyma cells do not form a continuous sheath surrounding a vessel),

(ii) Vasicentric (parenchyma cells encircle the vessels),

(iii) Abaxial (vasicentric parenchyma occurs more in width on abaxial side of vessel),

(iv) Adaxial (the parenchymatous sheath is more in width on adaxial side of vessel),

(v) Aliform (vasicentric parenchyma extends laterally in the form of wings), and

(vi) Confluent (vasicentric parenchyma extends and coalesces with other forming a continuous band) (Fig. 10.2).

The phylogenetic sequences among the distributional type of axial parenchyma are discussed below (Fig. 10.3).

1. The primitive wood may exhibit no parenchyma ex. vesselless wood of Winteraceae.

2. The primitive wood exhibits diffuse parenchyma. The cells of fusiform cambium differentiate into parenchyma.

3. The advanced form of wood exhibits diffuse-in-aggregate, where the tendency towards grouping of axial parenchyma is noticed.

4. The advanced form of wood exhibits apotracheal-banded parenchyma. The wide band of apotracheal parenchyma is considered to be more advanced than narrow band of parenchyma. It is assumed that diffuse-in- aggregate gives rise to narrow banded apotracheal type that ultimately forms wide band apotracheal type.

5. Marginal parenchyma (collective term of terminal and initial parenchyma) is formed as a result of changes in climatic conditions. So it is assumed that marginal parenchyma arose independently.

6. Scanty parenchyma seems to be less specialized than vasicentric.

7. The banded types gave rise to vasicentric, aliform and confluent types.

i. Origin of xylem fibre:

In primary xylem fibres originate from procambium whereas they are developed from fusiform initial of cambium in case of secondary xylem.

ii. Phylogeny of xylem fibre:

Fibres and tracheids are phylogenetically related and it is suggested that the former evolved from the latter. During evolution the length of fibre decreased, the bordered pits reduced in size and the thickness of cell wall increased. In secondary xylem of dicots, libriform fibre evolved in the sequence of tracheid, fibre-tracheid, and libriform fibre.

Bordered pits are prominent in tracheids. The pit border is diminished in fibre-tracheid where the bordered pits have less developed border. Disappearance of border on pit occurs in libriform fibre. Here the pits are simple or nearly so. The cell wall is thick in fibre-tracheid and thicker in libriform fibre. The diameter of fibre becomes narrower.


IPSC-derived homogeneous populations of developing schizophrenia cortical interneurons have compromised mitochondrial function

Schizophrenia (SCZ) is a neurodevelopmental disorder. Thus, studying pathogenetic mechanisms underlying SCZ requires studying the development of brain cells. Cortical interneurons (cINs) are consistently observed to be abnormal in SCZ postmortem brains. These abnormalities may explain altered gamma oscillation and cognitive function in patients with SCZ. Of note, currently used antipsychotic drugs ameliorate psychosis, but they are not very effective in reversing cognitive deficits. Characterizing mechanisms of SCZ pathogenesis, especially related to cognitive deficits, may lead to improved treatments. We generated homogeneous populations of developing cINs from 15 healthy control (HC) iPSC lines and 15 SCZ iPSC lines. SCZ cINs, but not SCZ glutamatergic neurons, show dysregulated Oxidative Phosphorylation (OxPhos) related gene expression, accompanied by compromised mitochondrial function. The OxPhos deficit in cINs could be reversed by Alpha Lipoic Acid/Acetyl-L-Carnitine (ALA/ALC) but not by other chemicals previously identified as increasing mitochondrial function. The restoration of mitochondrial function by ALA/ALC was accompanied by a reversal of arborization deficits in SCZ cINs. OxPhos abnormality, even in the absence of any circuit environment with other neuronal subtypes, appears to be an intrinsic deficit in SCZ cINs.

Conflict of interest statement

We do not have anything to disclose.

Figures

Fig. 1.. Generation of homogeneous population of…

Fig. 1.. Generation of homogeneous population of developmental cINs from HC and SCZ iPSCs

Fig. 2.. Oxidative phosphorylation pathway is significantly…

Fig. 2.. Oxidative phosphorylation pathway is significantly altered in developing SCZ cINs, but not in…

Fig. 3.. Multiple OxPhos genes are dysregulated…

Fig. 3.. Multiple OxPhos genes are dysregulated in developing SCZ cINs in expanded cohort

Fig 4.. Dysregulation of OxPhos genes in…

Fig 4.. Dysregulation of OxPhos genes in SCZ cINs resulted in defects in mitochondrial function.


Acknowledgements

We are grateful to B. Sheikh, M. Shvedunova, M. Buck, M. Samata, C. Pessoa Rodrigues, S. Lefkopoulos and G. Semplicio for critical reading of the manuscript. We thank E. Trompouki and R. Sawarkar for fruitful discussions and suggestions. We also thank P. Rawat for help with FRAP and M.-F. Basilicata for help with the generation of the Mof fl/- , Cre T/+ ESCs. The MPI-IE core facilities (for fluorescence-activated cell sorting, deep sequencing, imaging and mouse care), the EMBL IT facilities (for computing) and the EMBL EMCF (for electron microscopy) have been invaluable for this project. This work was supported by CRC992 (A02) and CRC1381 (B3) awarded to A.A., by an ERC Starting Grant awarded to J.O.K. (336045) and the Swiss National Science Foundation (SNSF 31003A_179418, to O.M.). E.A.R.-Z. is an Emmy Noether Fellow (DFG no. 396913060) P.K. acknowledges the ERC Advanced Grant CardioNect (201203).


Cell death shines a light on the origins of complex life

Organelles continue to thrive after the cells within which they exist die, a team of University of Bristol scientists have found, overturning previous assumptions that organelles decay too quickly to be fossilised.

As described in the journal Sciences Advances today [27 January], researchers from Bristol's School of Earth Sciences were able to document the decay process of eukaryotic algal cells, showing that nuclei, chloroplasts and pyrenoids (organelles found within chloroplasts) can persist for weeks and months after cell death in eukaryote cells, long enough to be preserved as fossils.

Emily Carlisle, a PhD student from Bristol's School of Earth Sciences and co-author, was able to characterise the transformation of the organelles into something resembling snot. She said: "I spent several weeks photographing algal cells as they decayed, checking the condition of the nuclei, chloroplasts and pyrenoids. From this, we could tell that these organelles don't decay immediately after cell death, but actually take many weeks to dissolve."

When life first appeared on Earth it was limited to simple bacteria. Two billion years later, complex life emerged in the form of large eukaryote cells with membrane-bound organelles, such as a nucleus and chloroplasts. The evolution of fungi, plants and animals followed.

However, precisely when complex life emerged has proved difficult to say. Previous genomic studies suggested that eukaryote cells could have evolved anywhere from 800 million to 1,800 million years ago, an imprecise range that needs fossils to narrow it down.

"The evolution of eukaryotes was a hugely important event in the history of life on Earth, but fossils of these cells are difficult to interpret," said Professor Phil Donoghue, expert in molecular palaeobiology and one of the co-authors of the study. "Some of them have structures that could be organelles, but there's long been this assumption that organelles cannot be preserved because they would decay too quickly."

Although living eukaryotes include large forms that are easily spotted, early eukaryotes were predominantly single cells, difficult to distinguish from bacterial cells.

Historically, large size and intricate cell walls have been used to identify early eukaryotes, but some bacteria can attain large size, and cell wall decorations might be lost to the ravages of time and erosion. Organelles such as nuclei and chloroplasts are not found in bacteria, and would therefore be a definitive indicator of complex life, but they have been assumed to decay too quickly to be fossilised.

The results of these experiments shed light on the controversial fossils of early complex life that include structures within the cells. Dr John Cunningham, a Bristol co-author, said: "The structures in Shuiyousphaeridium, a fossil from 1,700 million years ago, closely resemble nuclei. This interpretation has previously been dismissed because of the assumed rapid decay of nuclei. Our decay experiments have shown that nuclei can persist for several weeks, meaning the structures in Shuiyousphaeridium are likely to be nuclei."

By revealing the decay patterns of organelles, the study's authors say they can demonstrate the presence of complex life to 1,700 million years ago, helping to elucidate their evolutionary history with greater precision and clarity.


Digging for cellular fossils

Instead of digging through skeletal remains, Melnikov went digging through cells' ribosomal proteins to piece together their evolutionary history. (Ribosomes are cellular factories that help assemble proteins.)

"There are only a handful of genes that are ubiquitous," meaning they are present in all life forms, Melnikov said. About half of those conserved genes code for ribosomal proteins, he explained, a fact that suggests that the proteins have a lengthy evolutionary legacy, possibly stretching back to the beginning of life itself. In eukaryotes, ribosomal proteins enter the nucleus to be modified before setting up shop in the cytoplasm they enjoy easy access to the nucleus thanks to their NLSs.

By comparing the structure of ribosomal proteins sampled from all three domains of life &mdash Archaea, Bacteria and Eukarya &mdash Melnikov aimed to spot these signature sequences. The Archaea groups he investigated are among those that can be found in nature today.

Lo and behold, Melnikov and his colleagues unearthed four archaeal proteins equipped with security badges similar to their eukaryotic counterparts. NLS-like sequences appeared in multiple groups of Archaea, so the researchers deduced that the feature had appeared early in archaeal evolutionary history. (In Archaea, however, the NLS probably mainly help the organisms more easily identify nucleic acids, the building blocks of DNA and RNA. While eukaryotic NLSs also serve this function, they are better known for helping proteins into the nucleus.)

The team went on to test whether the NLSs were functionally interchangeable across kingdoms of life, swapping out a eukaryotic badge for an archaeal one. Beneath a light microscope, the archaeal NLSs appeared to work just like eukaryotic NLSs and granted their associated proteins VIP access to the nucleus. Despite sharing the same functions, the NLSs in eukaryotes and Archaea may not be evolutionarily related, experts say.

Iyer, for instance, remains dubious of the finding. NLSs are made up of just five to six protein building blocks, called amino acids. Due to their short length and particular chemical structure, NLSs are statistically likely to appear in proteins by mere chance, Iyer told Live Science.

In other words, the archaeal and eukaryotic sequences may have popped up independently and therefore would not be evolutionarily related. Iyer said he'd be more convinced if further research uncovers archaeal NLSs in additional proteins, ones similar to those that enter the nucleus in eukaryotes.

"In the end, this just shows that these [NLS-like] sequences likely preceded nuclei," Buzz Baum, a cell and evolutionary biologist at the MRC Laboratory for Molecular Cell Biology in England, told Live Science in an email. Archaea that share many genetic similarities with modern eukaryotes still lack nuclei and organelles, he explained, so it&rsquos hard to see how these NLSs led to the development of nuclei.


Abstract

The confinement of crystallizable blocks within AB or ABC microphase-separated block copolymers in the nanoscopic scale can be tailored by adequate choice of composition, molecular weight, and chemical structure. In this work we have examined the crystallization behavior of a series of AB and ABC block copolymers incorporating one or two of the following crystallizable blocks: polyethylene, poly(ε-caprolactone), and poly(ethylene oxide). The density of confined microdomain structures (MD) within block copolymers of specific compositions, in cases where the MD are dispersed as spheres, cylinders, or any other isolated morphology, is much higher than the number of heterogeneities available in each crystallizable block. Therefore, fractionated crystallization takes place with one or several crystallization steps at decreasing temperatures. In specific cases, the clear observation of exclusive crystallization from homogeneous nuclei was obtained. The results show that, regardless of the specific morphological features of the MD, it is their vast number as compared to the number of heterogeneities present in the system that determines the fractionated character of the crystallization or in extreme cases homogeneous nucleation. The self-nucleation behavior was also found to depend on the composition of the copolymers. When the crystallizable block is confined into spheres or cylinders and exhibits homogeneous nucleation, the self-nucleation domain disappears. This is a direct consequence of the extremely high density of microdomain structures that need to be self-seeded (on the order of 10 15 −10 16 /cm 3 ). Therefore, to increase the density of self-nuclei, the self-nucleation temperature has to be decreased to values so low that extensive partial melting is achieved, and some of the unmelted crystal fragments can be annealed, in some cases even before self-nucleation takes place.

This work is dedicated to the memory of our friend and colleague Prof. Reimund Stadler.


DNA-peptide interactions create complex behaviors which may have helped shape biology

Deoxyribonucleic acid (DNA)-protein interactions are extremely important in biology. For example, each human cell contains about 2 meters worth of DNA, but this is packaged into a space about one million times smaller. The information in this DNA allows the cell to copy itself. This extreme packaging is mainly accomplished in cells by wrapping the DNA around proteins. Thus, how DNA and proteins interact is of extreme interest to scientists trying to understand how biology organises itself. New research by scientists at the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology and the Institut Pierre-Gilles de Gennes, ESPCI Paris, Université PSL suggests that the interactions of DNA and proteins have deep-seated propensities to form higher-ordered structures such as those which allow the extreme packaging of DNA in cells.

Modern living cells are principally composed of a few classes of large molecules. DNA gets the lion's share of attention as it is the repository of the information cells use to build themselves generation after generation. This information-rich DNA is normally present as a double-stranded caduceus of two polymers wrapped around each other, with much of what makes the information DNA contains obscured to the external environment because the information-bearing parts of the molecules are engaged with their complementary strand. When DNA is copied into ribonucleic acid (RNA), its strands are pulled apart to allow its more complex surfaces to interact, which enables it to be copied into single-stranded RNA polymers. These RNA polymers are finally read out by biological processes into proteins, which are polymers of a variety of amino acids with extremely complicated surface properties. Thus, DNA and RNA are somewhat predictable in terms of their chemical behaviour as polymers, while proteins are not.

Polymeric molecules, those composed or repeated types of subunits, can display complex behaviours when mixed with other chemicals, especially when dissolved in a solvent like water. Chemists have developed a complex set of terms for how compounds behave when they are mixed. For example, the proteins in cow's milk are considered a colloidal (or homogeneous noncrystalline suspended mixture which does not settle and cannot be separated by physical means) suspension in water. When lemon juice is added to milk, the suspended proteins reorganise themselves to produce the visible self-organisation of curds, which do separate into a new phase. There are other types of this phenomenon chemists have discovered over the years, for example, liquid crystals (LC). LCs are formed when a molecules have an elongated shape or the tendency to make linear aggregates (like stacks of molecules one on top of each other): the resulting material presents a mixture of the properties of a crystal and a liquid: the material thus has a certain degree of order like a solid (for example, parallel orientation of the molecules) but still retains its fluidity (molecules can easily slip on and by each other). We all experience liquid crystals in the various screens we interact with every day "LCDs," or liquid crystal displays, which use these variable properties to make the images we see on our device screens. In their work, Fraccia and Jia, showed that double-stranded DNA and peptides can generate many different LC phases in a very peculiar way: the LCs actually form in membraneless droplets, called coacervates, where DNA and peptides are spontaneously co-assembled and ordered. This process brings DNA and peptides to very high concentrations, comparable to that of a cell's nucleus, which is 100-1000 times greater of that of the very diluted initial solution (which is the maximum concentration that can likely be achieved on early Earth). Thus, such spontaneous behaviour can in principle favour the formation of the first cell-like structures on early Earth, which would take advantage of the ordered, but fluid, LC matrix in order to gain stability and functionality, and to favour the growth and the evolution of primitive biomolecules.

The cut-off between when these higher-order properties begin to present themselves is not always clear cut. When molecules interact at the molecular level, they often "self-organise." One can think of the process of adding sand to a sandpile: as one sprinkles more and more sand to a pile, it tends to form a "low energy" final state -- a pile. Though the addition of sand grains may cause some new structures to form locally, at some point, the addition of one more grain causes a landslide in the pile which reinforces the conical shape of the pile.

Though we all benefit from the existence of these phenomena, the scientific community may be missing important aspects of the implications of this type of self-organisation, Jia and Fraccia argue. The combination of these collective material self-organising effects may be relevant at many scales of biology and may be important for biomolecular structure transitions in cell physiology and disease. In particular, the researchers discovered that various liquid crystalline structures could be accessed continuously simply by changes in environmental conditions, even as simple as changes in salinity or temperature given the numerous unexplored conditions, this work suggests many more novel self-organised LC mesophases with potential biological function could be discovered in the near future.

This new understanding of biopolymeric self-organisation may also be important for understanding how life self-organised to become living in the first place. Understanding how primitive collections of molecules could have structured themselves into collectively behaving aggregates is a significant avenue of future research.

"When the general public hears about liquid crystals, they might think of TV screens and engineering applications. However, very few would immediately think of basic science. Most researchers would not even make the connection between LCs and the origins of life. We hope this work will help increase the public's understanding of LCs in the context of the origins of life," says co-author Jia.

Finally, this work may also be relevant to disease. For example, recent discoveries regarding diseases including Alzheimer's, Parkinson's, Huntington's Disease, and ALS (Lou Gehrig's Disease) have pointed to intracellular phase transitions and separation leading to membraneless droplets as potential major causes.

The researchers noted that though their work was heavily impacted by the pandemic, they did their best to keep working under the global shutdowns and travel restrictions.