Confinement in fibrous environments positions and orients mitotic spindles.

Accurate positioning of the mitotic spindle within the rounded cell body is critical to physiological maintenance. Adherent mitotic cells encounter confinement from neighboring cells or the extracellular matrix (ECM), which can cause rotation of mitotic spindles and, consequently, titling of the metaphase plate (MP). To understand the positioning and orientation of mitotic spindles under confinement by fibers (ECM-confinement), we use flexible ECM-mimicking nanofibers that allow natural rounding of the cell body while confining it to differing levels. Rounded mitotic bodies are anchored in place by actin retraction fibers (RFs) originating from adhesion clusters on the ECM-mimicking fibers. We discover the extent of ECM-confinement patterns RFs in 3D: triangular and band-like at low and high confinement, respectively. A stochastic Monte-Carlo simulation of the centrosome (CS), chromosome (CH), membrane interactions, and 3D arrangement of RFs on the mitotic body recovers MP tilting trends observed experimentally. Our mechanistic analysis reveals that the 3D shape of RFs is the primary driver of the MP rotation. Under high ECM-confinement, the fibers can mechanically pinch the cortex, causing the MP to have localized deformations at contact sites with fibers. Interestingly, high ECM-confinement leads to low and high MP tilts, which mechanistically depend upon the extent of cortical deformation, RF patterning, and MP position. We identify that cortical deformation and RFs work in tandem to limit MP tilt, while asymmetric positioning of MP leads to high tilts. Overall, we provide fundamental insights into how mitosis may proceed in fibrous ECM-confining microenvironments in vivo.

Starch spectra of Ampelopteris prolifera (Retz.) Copel, a new addition to the existing lexicon and its comparison with a local potato cultivar (Solanum tuberosum L. cv. Kufri Jyoti).

Novel kinds of starch spectra were generated from a lesser-known plant, making this investigation unique. The recent trend of starch characterization shows the establishment of novel bioresources from nonconventional unexplored databases. The present endeavor was made to obtain the starch fingerprint of Ampelopteris prolifera (rhizome) belonging to seedless vascular plants. For comparison, a commercial local cultivar of potato (Kufri Jyoti) was taken. The starch particle of A. prolifera shows much uniqueness depicting its novelty viz., crystallinity index of 60.04 %, powder diffractogram at (2θ scale)17.57° to 39.78°; this diffractogram pattern is reported from this study as newer one i.e. R type(whereas potato starch is CB type); characteristic peak at 2θ = 20.07° suggests starch-lipid complex formation and V type crystallinity (i.e. RS 5 type); FTIR spectra showing the presence of more short chain branching; high gelatinization temperature(84.62 ±â€¯0.10), particle size and zeta value of A. prolifera is 4.00 ±â€¯0.81 µm and - 18.91 ±â€¯3.58 mV respectively. Bragg's peak from the single crystal X-ray diffraction has been generated for the first time of A. prolifera. Extraction of the starch particle was performed in chilled water. Therefore, the present study suggests wide-spectrum commercial utility and cost-effective production.

CKAP5 stabilizes CENP-E at kinetochores by regulating microtubule-chromosome attachments.

Stabilization of microtubule plus end-directed kinesin CENP-E at the metaphase kinetochores is important for chromosome alignment, but its mechanism remains unclear. Here, we show that CKAP5, a conserved microtubule plus tip protein, regulates CENP-E at kinetochores in human cells. Depletion of CKAP5 impairs CENP-E localization at kinetochores at the metaphase plate and results in increased kinetochore-microtubule stability and attachment errors. Erroneous attachments are also supported by computational modeling. Analysis of CKAP5 knockout cancer cells of multiple tissue origins shows that CKAP5 is preferentially essential in aneuploid, chromosomally unstable cells, and the sensitivity to CKAP5 depletion is correlated to that of CENP-E depletion. CKAP5 depletion leads to reduction in CENP-E-BubR1 interaction and the interaction is rescued by TOG4-TOG5 domain of CKAP5. The same domain can rescue CKAP5 depletion-induced CENP-E removal from the kinetochores. Interestingly, CKAP5 depletion facilitates recruitment of PP1 to the kinetochores and furthermore, a PP1 target site-specific CENP-E phospho-mimicking mutant gets stabilized at kinetochores in the CKAP5-depleted cells. Together, the results support a model in which CKAP5 controls mitotic chromosome attachment errors by stabilizing CENP-E at kinetochores and by regulating stability of the kinetochore-attached microtubules.

Recent Advances in the Phytochemistry of Bryophytes: Distribution, Structures and Biological Activity of Bibenzyl and Bisbibenzyl Compounds.

Research on bryophyte phytochemistry has revealed the presence of different phytochemicals like fatty acids, terpenoids, small phenolic molecules, etc. Small phenolic molecules, i.e., bibenzyls (of two aromatic rings) and bisbibenzyls (four aromatic rings), are unique signature molecules of liverworts. The first bisbibenzyls marchantin A and riccardin A were discovered in two consecutive years, i.e., 1982 and 1983, respectively, by Asakawa and coworkers. Since then, about 70 bisbibenzyls have been reported. These molecules are characterized and identified using different spectroscopic techniques and surveyed for different bioactivity and structure-activity relations. Biochemistry is determined by the season, geography, and environment. In this review, quantitative and qualitative information on bibenzyls and bisbibenzyl compounds and their distribution in different liverworts across, geographies along withtraditional to advanced extraction methods, and characterization techniques are summarized. Also, a comprehensive account of characteristic spectra of different bisbibenzyl compounds, their subtypes, and their basic skeleton patterns are compared. A comprehensive table is provided here for the first time presenting the quantity of bibenzyls, bisbenzyls, and their derivatives found in bryophytes, mentioning the spectroscopic data and mass profiles of the compounds. The significance of these compounds in different bioactivities like antibiotic, antioxidative, antitumor, antivenomous, anti-influenza, insect antifeedant, cytotoxic, and anticancerous activities are surveyed and critically enumerated.

Microtubule search-and-capture model evaluates the effect of chromosomal volume conservation on spindle assembly during mitosis.

Variation in the chromosome numbers can arise from the erroneous mitosis or fusion and fission of chromosomes. While the mitotic errors lead to an increase or decrease in the overall chromosomal substance in the daughter cells, fission and fusion keep this conserved. Variations in chromosome numbers are assumed to be a crucial driver of speciation. For example, the members of the muntjac species are known to have very different karyotypes with the chromosome numbers varying from 2n=70+3B in the brown brocket deer to 2n=46 in the Chinese muntjac and 2n=6/7 in the Indian muntjac. The chromosomal content in the nucleus of these closely related mammals is roughly the same and various chromosome fusion and fission pathways have been suggested as the evolution process of these karyotypes. Similar trends can also be found in lepidoptera and yeast species which show a wide variation of chromosome numbers. The effect of chromosome number variation on the spindle assembly time and accuracy is still not properly addressed. We computationally investigate the effect of conservation of the total chromosomal substance on the spindle assembly during prometaphase. Our results suggest that chromosomal fusion pathways aid the microtubule-driven search and capture of the kinetochore in cells with monocentric chromosomes. We further report a comparative analysis of the site and percentage of amphitelic captures, dependence on cell shape, and position of the kinetochore in respect to chromosomal volume partitioning.

Jamming and flocking in the restricted active Potts model.

We study the active Potts model with either site occupancy restriction or on-site repulsion to explore jamming and kinetic arrest in a flocking model. The incorporation of such volume exclusion features leads to a surprisingly rich variety of self-organized spatial patterns. While bands and lanes of moving particles commonly occur without or under weak volume exclusion, strong volume exclusion along with low temperature, high activity, and large particle density facilitates jams due to motility-induced phase separation. Through several phase diagrams, we identify the phase boundaries separating the jammed and free-flowing phases and study the transition between these phases which provide us with both qualitative and quantitative predictions of how jamming might be delayed or dissolved. We further formulate and analyze a hydrodynamic theory for the restricted APM which predicts various features of the microscopic model.

Mechanistic model for nuclear migration in hyphae during mitosis.

Saccharomyces cerevisiae and Candida albicans, the two well-known human pathogens, can be found in all three morphologies, i.e., yeast, pseudohyphae, and true hyphae. The cylindrical daughter-bud (germ tube) grows very long for true hyphae, and the cell cycle is delayed compared to the other two morphologies. The place of the nuclear division is specific for true hyphae determined by the position of the septin ring. However, the septin ring can localize anywhere inside the germ tube, unlike the mother-bud junction in budding yeast. Since the nucleus often migrates a long path in the hyphae, the underlying mechanism must be robust for executing mitosis in a timely manner. We explore the mechanism of nuclear migration through hyphae in light of mechanical interactions between astral microtubules and the cell cortex. We report that proper migration through constricted hyphae requires a large dynein pull applied on the astral microtubules from the hyphal cortex. This is achieved when the microtubules frequently slide along the hyphal cortex so that a large population of dyneins actively participate, pulling on them. Simulation shows timely migration when the dyneins from the mother cortex do not participate in pulling on the microtubules. These findings are robust for long migration and positioning of the nucleus in the germ tube at the septin ring.

Self-organized criticality of magnetic avalanches in disordered ferrimagnetic material.

We observe multiple steplike jumps in a Dy-Fe-Ga-based ferrimagnetic alloy in its magnetic hysteresis curve at 2 K. The observed jumps are found to have a stochastic character with respect to their magnitude and the field position, and the jumps do not correlate with the duration of the field. The distribution of jump size follows a power law variation indicating the scale invariance nature of the jumps. We have invoked a simple two-dimensional random bond Ising-type spin system to model the dynamics. Our computational model can qualitatively reproduce the jumps and their scale-invariant character. It also elucidates that the flipping of antiferromagnetically coupled Dy and Fe clusters is responsible for the observed jumps in the hysteresis loop. These features are described in terms of the self-organized criticality.

Mitotic outcomes and errors in fibrous environments.

During mitosis, cells round up and utilize the interphase adhesion sites within the fibrous extracellular matrix (ECM) as guidance cues to orient the mitotic spindles. Here, using suspended ECM-mimicking nanofiber networks, we explore mitotic outcomes and error distribution for various interphase cell shapes. Elongated cells attached to single fibers through two focal adhesion clusters (FACs) at their extremities result in perfect spherical mitotic cell bodies that undergo significant 3-dimensional (3D) displacement while being held by retraction fibers (RFs). Increasing the number of parallel fibers increases FACs and retraction fiber-driven stability, leading to reduced 3D cell body movement, metaphase plate rotations, increased interkinetochore distances, and significantly faster division times. Interestingly, interphase kite shapes on a crosshatch pattern of four fibers undergo mitosis resembling single-fiber outcomes due to rounded bodies being primarily held in position by RFs from two perpendicular suspended fibers. We develop a cortex-astral microtubule analytical model to capture the retraction fiber dependence of the metaphase plate rotations. We observe that reduced orientational stability, on single fibers, results in increased monopolar mitotic defects, while multipolar defects become dominant as the number of adhered fibers increases. We use a stochastic Monte Carlo simulation of centrosome, chromosome, and membrane interactions to explain the relationship between the observed propensity of monopolar and multipolar defects and the geometry of RFs. Overall, we establish that while bipolar mitosis is robust in fibrous environments, the nature of division errors in fibrous microenvironments is governed by interphase cell shapes and adhesion geometries.

Mechanics of microtubule organizing center clustering and spindle positioning in budding yeast Cryptococcus neoformans.

The dynamic process of mitotic spindle assembly depends on multitudes of inter-dependent interactions involving kinetochores (KTs), microtubules (MTs), spindle pole bodies (SPBs), and molecular motors. Before forming the mitotic spindle, multiple visible microtubule organizing centers (MTOCs) coalesce into a single focus to serve as an SPB in the pathogenic budding yeast, Cryptococcus neoformans. To explain this unusual phenomenon in the fungal kingdom, we propose a "search and capture" model, in which cytoplasmic MTs (cMTs) nucleated by MTOCs grow and capture each other to promote MTOC clustering. Our quantitative modeling identifies multiple redundant mechanisms mediated by a combination of cMT-cell cortex interactions and inter-cMT coupling to facilitate MTOC clustering within the physiological time limit as determined by time-lapse live-cell microscopy. Besides, we screen various possible mechanisms by computational modeling and propose optimal conditions that favor proper spindle positioning-a critical determinant for timely chromosome segregation. These analyses also reveal that a combined effect of MT buckling, dynein pull, and cortical push maintains spatiotemporal spindle localization.

Studying the progress of COVID-19 outbreak in India using SIRD model.

We explore a standard epidemiological model, known as the SIRD model, to study the COVID-19 infection in India, and a few other countries around the world. We use (a) the stable cumulative infection of various countries and (b) the number of infection versus the tests carried out to evaluate the model. The time-dependent infection rate is set in the model to obtain the best fit with the available data. The model is simulated aiming to project the probable features of the infection in India, various Indian states, and other countries. India imposed an early lockdown to contain the infection that can be treated by its healthcare system. We find that with the current infection rate and containment measures, the total active infection in India would be maximum at the end of June or beginning of July 2020. With proper containment measures in the infected zones and social distancing, the infection is expected to fall considerably from August. If the containment measures are relaxed before the arrival of the peak infection, more people from the susceptible population will fall sick as the infection is expected to see a threefold rise at the peak. If the relaxation is given a month after the peak infection, a second peak with a moderate infection will follow. However, a gradual relaxation of the lockdown started well ahead of the peak infection, leads to a nearly twofold increase of the peak infection with no second peak. The model is further extended to incorporate the infection arising from the population showing no symptoms. The preliminary finding suggests that random testing needs to be carried out within the asymptomatic population to contain the spread of the disease. Our model provides a semi-quantitative overview of the progression of COVID-19 in India, with model projections reasonably replicating the current progress. The projection of the model is highly sensitive to the choice of the parameters and the available data.

SEIRD model to study the asymptomatic growth during COVID-19 pandemic in India.

According to the current perception, symptomatic, presymptomatic and asymptomatic infectious persons can infect the healthy population susceptible to the SARS-CoV-2. More importantly, various reports indicate that the number of asymptomatic cases can be several-fold higher than the reported symptomatic cases. In this article, we take the reported cases in India and various states within the country till September 1, as the specimen to understand the progression of the COVID-19. Employing a modified SEIRD model, we predict the spread of COVID-19 by the symptomatic as well as asymptomatic infectious population. Considering reported infection primarily due to symptomatic, we compare the model predicted results with the available data to estimate the dynamics of the asymptomatically infected population. Our data indicate that in the absence of the asymptomatic infectious population, the number of symptomatic cases would have been much less. Therefore, the current progress of the symptomatic infection can be reduced by quarantining the asymptomatically infectious population via extensive or random testing. This study is motivated strictly toward academic pursuit; this theoretical investigation is not meant for influencing policy decisions or public health practices.

Flocking with a q-fold discrete symmetry: Band-to-lane transition in the active Potts model.

We study the q-state active Potts model (APM) on a two-dimensional lattice in which self-propelled particles have q internal states corresponding to the q directions of motion. A local alignment rule inspired by the ferromagnetic q-state Potts model and self-propulsion via biased diffusion according to the internal particle states elicits collective motion at high densities and low noise. We formulate a coarse-grained hydrodynamic theory with which we compute the phase diagrams of the APM for q=4 and q=6 and analyze the flocking dynamics in the coexistence region, where the high-density (polar liquid) phase forms a fluctuating stripe of coherently moving particles on the background of the low-density (gas) phase. A reorientation transition of the phase-separated profiles from transversal band motion to longitudinal lane formation is found, which is absent in the Vicsek model and the active Ising model. The origin of this reorientation transition is revealed by a stability analysis: for large velocities the transverse diffusivity approaches zero and stabilizes lanes. Computer simulations corroborate the analytical predictions of the flocking and reorientation transitions and validate the phase diagrams of the APM.

Mechanics of Multicentrosomal Clustering in Bipolar Mitotic Spindles.

To segregate chromosomes in mitosis, cells assemble a mitotic spindle, a molecular machine with centrosomes at two opposing cell poles and chromosomes at the equator. Microtubules and molecular motors connect the poles to kinetochores, specialized protein assemblies on the centromere regions of the chromosomes. Bipolarity of the spindle is crucial for the proper cell division, and two centrosomes in animal cells naturally become two spindle poles. Cancer cells are often multicentrosomal, yet they are able to assemble bipolar spindles by clustering centrosomes into two spindle poles. Mechanisms of this clustering are debated. In this study, we computationally screen effective forces between 1) centrosomes, 2) centrosomes and kinetochores, 3) centrosomes and chromosome arms, and 4) centrosomes and cell cortex to understand mechanics that determines three-dimensional spindle architecture. To do this, we use the stochastic Monte Carlo search for stable mechanical equilibria in the effective energy landscape of the spindle. We find that the following conditions have to be met to robustly assemble the bipolar spindle in a multicentrosomal cell: 1) the strengths of centrosomes' attraction to each other and to the cell cortex have to be proportional to each other and 2) the strengths of centrosomes' attraction to kinetochores and repulsion from the chromosome arms have to be proportional to each other. We also find that three other spindle configurations emerge if these conditions are not met: 1) collapsed, 2) monopolar, and 3) multipolar spindles, and the computational screen reveals mechanical conditions for these abnormal spindles.

Ordering kinetics in a q-state random-bond clock model: Role of vortices and interfaces.

In this article, we present a Monte Carlo study of phase transition and coarsening dynamics in the nonconserved two-dimensional random-bond q-state clock model (RBCM) deriving from a pure clock model [Chatterjee et al., Phys. Rev. E 98, 032109 (2018)10.1103/PhysRevE.98.032109]. Akin to the pure clock model, RBCM also passes through two different phases when quenched from a disordered initial configuration representing at infinite temperature. Our investigation of the equilibrium phase transition affirms that both upper (T_{c}^{1}) and lower (T_{c}^{2}) phase transition temperatures decrease with bond randomness strength ε. Effect of ε on the nonequilibrium coarsening dynamics is investigated following independent rapid quenches in the quasi-long-range ordered (QLRO, T_{c}^{2}

A novel combinatorial approach of quantitative microscopy and in silico modeling deciphers Arf1-dependent Golgi size regulation.

Regulation of organelle size and shape is a poorly understood but fascinating subject. Several theoretical studies were reported on Golgi size regulation, but a combination of experimental and theoretical approaches is rare. In combination with the quantitative microscopy and a coarse-grained simulation model, we have developed a technique to gain insights into the functions of potential regulators of Golgi size in budding yeast Saccharomyces cerevisiae. To validate our method, we tested wild-type and arf1[Formula: see text] strain harboring early and late Golgi cisternae labeled with green and red fluorescent fusions. Our concentration-dependent maturation model prediction concurs with most of the experimental results for both wild-type and arf1[Formula: see text] strains. Decisive match of simulation and experimental data provide insight into such specific factor's function in regulating the Golgi size. Details of the complex multifactorial network of Golgi size regulation can be deciphered in the future using a similar combination of quantitative microscopy and in silico model.

Search and Capture Efficiency of Dynamic Microtubules for Centrosome Relocation during IS Formation.

Upon contact with antigen-presenting cells, cytotoxic T lymphocytes (T cells) establish a highly organized contact zone denoted as the immunological synapse (IS). The formation of the IS implies relocation of the microtubule organizing center (MTOC) toward the contact zone, which necessitates a proper connection between the MTOC and the IS via dynamic microtubules (MTs). The efficiency of the MTs finding the IS within the relevant timescale is, however, still illusive. We investigate how MTs search the three-dimensional constrained cellular volume for the IS and bind upon encounter to dynein anchored at the IS cortex. The search efficiency is estimated by calculating the time required for the MTs to reach the dynein-enriched region of the IS. In this study, we develop simple mathematical and numerical models incorporating relevant components of a cell and propose an optimal search strategy. Using the mathematical model, we have quantified the average search time for a wide range of model parameters and proposed an optimized set of values leading to the minimal capture time. Our results show that search times are minimal when the IS formed at the nearest or at the farthest sites on the cell surface with respect to the perinuclear MTOC. The search time increases monotonically away from these two specific sites and is maximal at an intermediate position near the equator of the cell. We observed that search time strongly depends on the number of searching MTs and distance of the MTOC from the nuclear surface.

Mechanistic three-dimensional model to study centrosome positioning in the interphase cell.

During the interphase in mammalian cells, the position of the centrosome is actively maintained at a small but finite distance away from the nucleus. The perinuclear positioning of the centrosome is crucial for cellular trafficking and progression into mitosis. Although the literature suggests that the contributions of the microtubule-associated forces bring the centrosome to the center of the cell, the position of the centrosome was merely investigated in the absence of the nucleus. Upon performing a coarse-grained simulation study with mathematical analysis, we show that the combined effect of the forces due to the cell cortex and the nucleus facilitate the centrosome positioning. Our study also demonstrates that in the absence of nucleus-based forces, the centrosome collapses on the nucleus due to cortical forces. Depending upon the magnitudes of the cortical forces and the nucleus-based forces, the centrosome appears to stay at various distances away from the nucleus. Such null force regions are found to be stable as well as unstable fixed points. This study uncovers a set of redundant schemes that the cell may adopt to produce the required cortical and nucleus-based forces stabilizing the centrosome at a finite distance away from the nucleus.

Spatio-temporal regulation of nuclear division by Aurora B kinase Ipl1 in Cryptococcus neoformans.

The nuclear division takes place in the daughter cell in the basidiomycetous budding yeast Cryptococcus neoformans. Unclustered kinetochores gradually cluster and the nucleus moves to the daughter bud as cells enter mitosis. Here, we show that the evolutionarily conserved Aurora B kinase Ipl1 localizes to the nucleus upon the breakdown of the nuclear envelope during mitosis in C. neoformans. Ipl1 is shown to be required for timely breakdown of the nuclear envelope as well. Ipl1 is essential for viability and regulates structural integrity of microtubules. The compromised stability of cytoplasmic microtubules upon Ipl1 depletion results in a significant delay in kinetochore clustering and nuclear migration. By generating an in silico model of mitosis, we previously proposed that cytoplasmic microtubules and cortical dyneins promote atypical nuclear division in C. neoformans. Improving the previous in silico model by introducing additional parameters, here we predict that an effective cortical bias generated by cytosolic Bim1 and dynein regulates dynamics of kinetochore clustering and nuclear migration. Indeed, in vivo alterations of Bim1 or dynein cellular levels delay nuclear migration. Results from in silico model and localization dynamics by live cell imaging suggests that Ipl1 spatio-temporally influences Bim1 or/and dynein activity along with microtubule stability to ensure timely onset of nuclear division. Together, we propose that the timely breakdown of the nuclear envelope by Ipl1 allows its own nuclear entry that helps in spatio-temporal regulation of nuclear division during semi-open mitosis in C. neoformans.

EB1 regulates attachment of Ska1 with microtubules by forming extended structures on the microtubule lattice.

Kinetochore couples chromosome movement to dynamic microtubules, a process that is fundamental to mitosis in all eukaryotes but poorly understood. In vertebrates, spindle-kinetochore-associated (Ska1-3) protein complex plays an important role in this process. However, the proteins that stabilize Ska-mediated kinetochore-microtubule attachment remain unknown. Here we show that microtubule plus-end tracking protein EB1 facilitates Ska localization on microtubules in vertebrate cells. EB1 depletion results in a significant reduction of Ska1 recruitment onto microtubules and defects in mitotic chromosome alignment, which is also reflected in computational modelling. Biochemical experiments reveal that EB1 interacts with Ska1, facilitates Ska1-microtubule attachment and together stabilizes microtubules. Structural studies reveal that EB1 either with Ska1 or Ska complex forms extended structures on microtubule lattice. Results indicate that EB1 promotes Ska association with K-fibres and facilitates kinetochore-microtubule attachment. They also implicate that in vertebrates, chromosome coupling to dynamic microtubules could be mediated through EB1-Ska extended structures.