Biology subjects

Hernandez-Herrera, P.

Publications and source records attributed to Hernandez-Herrera, P..

7 recordsLinked to original sources

bioRxiv2025

Presynaptic Actin Nanostructures: A Reproducibility Case Study

In an effort to assess the reproducibility of bioimage analyses in current publications, we took part in a Global BioImage Analysts Society (GloBIAS) initiative to try and reproduce results from published articles. We attempted to reproduce core findings from the work of Bingham et al., which investigates the actin organisation in presynaptic structures by using diffraction-limited and super-resolution microscopy. While the original paper unveiled clear biological insight, it lacked sufficient detail in the bioimage analysis methodological approach, limiting the depth of reproducibility we could achieve. Through frequent contacts with the corresponding author, we managed to replicate qualitative aspects of the analysis of actin nanostructures in bead-induced presynapses. We performed image reconstruction from super-resolution microscopy data, automatic image registration and visual inspection, followed by manual annotation of structures of interest in [~]35 images. Our experience with this exercise highlights the importance of transparent data sharing and accessibility, as well as the need to adhere to bioimage analysis standards that ensure the reproducibility of nowadays complex biological image analysis studies. It also shows how crucial interdisciplinary collaboration is, since many biology labs are simply unaware of these standards, which are often easy to implement and would likely be widely adopted if their value was better understood or known.

neuroscience↗

bioRxiv2024

Fluid flow reconstruction around a free-swimming sperm in 3D

We investigate the dynamics and hydrodynamics of a human spermatozoa swimming freely in 3D. We simultaneously track the sperm flagellum and the sperm head orientation in the laboratory frame of reference via high-speed high-resolution 4D (3D+t) microscopy, and extract the flagellar waveform relative to the body frame of reference, as seen from a frame of reference that translates and rotates with the sperm in 3D. Numerical fluid flow reconstructions of sperm motility are performed utilizing the experimental 3D waveforms, with excellent accordance between predicted and observed 3D sperm kinematics. The reconstruction accuracy is validated by directly comparing the three linear and three angular sperm velocities with experimental measurements. Our microhydrodynamic analysis reveals a novel fluid flow pattern, characterized by a pair of vortices that circulate in opposition to each other along the sperm cell. Finally, we show that the observed sperm counter-vortices are not unique to the experimental beat, and can be reproduced by idealised waveform models, thus suggesting a fundamental flow structure for free-swimming sperm propelled by a 3D beating flagellum.

biophysics↗

bioRxiv2023

Feature-Based 3D+t Descriptors of Hyperactivated Human Sperm Beat Patterns

The flagellar movement of the mammalian sperm is essential for male fertility as it enables this cell to reach and fertilize an egg. In the female reproductive tract, human spermatozoa undergo a process called capacitation which promotes changes in their motility. Only those spermatozoa that change to hyperactivated (HA) motility are capable of fertilizing the egg; this type of motility is characterized by asymmetric flagellar bends of greater amplitude and lower frequency. Historically, clinical fertilization studies have used two-dimensional analysis to classify sperm motility, although, sperm motility is three-dimensional (3D). Recent studies have described several 3D beating features of sperm flagella, including curvature, torsion, and asymmetries. However, the 3D motility pattern of hyperactivated spermatozoa has not yet been characterized. One of the main difficulties in classifying these patterns in 3D is the lack of a ground-truth reference, as it can be difficult to visually assess differences in flagellar beat patterns. Additionally, only about 10 - 20% of sperm that have been induced to capacitate are truly capacitated (i.e., hyperactivated). In this work, we used an image acquisition system that can acquire, segment, and track sperm flagella in 3D+t. We developed a feature-based vector that describes the spatio-temporal flagellar sperm motility patterns by an envelope of ellipses. Our results demonstrate that the proposed descriptors can effectively be used to distinguish between hyperactivated and nonhyperactivated spermatozoa, providing a tool to characterize the 3D sperm flagellar beat motility patterns without prior training or supervision. We demonstrated the effectiveness of the descriptors by applying them to a dataset of human sperm cells and showing that they can accurately classify the motility patterns of the sperm cells. This work is potentially useful for assessing male fertility or for diagnosing.

bioengineering↗

bioRxiv2022

The human sperm head spins with a conserved direction during swimming in 3D

In human sperm, head spinning is essential for sperm swimming and critical for fertilization. Measurement of head spinning has not been straightforward due to its symmetric head morphology, its translucent nature and fast 3D motion driven by its helical flagellum movement. Microscope image acquisition has been mostly restricted to 2D single focal plane images limited to head position tracing, in absence of head orientation and rotation in 3D. To date, human sperm spinning has been reported to be mono or bidirectional, and even intermittently changing direction. This variety in head spinning direction, however, appears to contradict observations of conserved helical beating of the human sperm flagellum. Here, we reconcile these observations by directly measuring the head spinning movement of freely swimming human sperm with multi-plane 4D microscopy. We show that 2D microscopy is unable to distinguish the spinning direction in human sperm. We evaluated the head spinning of 409 spermatozoa in four different conditions: in non-capacitating and capacitating solutions, for both aqueous and viscous media. All spinning spermatozoa, regardless of the experimental conditions spun counterclockwise (CCW) as seen from head-to-tail. Head spinning was suppressed in 57% of spermatozoa swimming in non-capacitating viscous media, though, interestingly, they recovered the CCW spinning after incubation in capacitating conditions within the same viscous medium. Our observations show that the spinning direction in human sperm is conserved, even when recovered from non-spin, indicating the presence of a robust and persistent helical driving mechanism powering the human sperm flagellum, thus of critical importance in future sperm motility assessments, human reproduction research and microorganism self-organised swimming.

cell biology↗

bioRxiv2022

Fluorescence fluctuation based super resolution microscopy, basic concepts for an easy start.

Due to the wave nature of light, optical microscopy has a lower-bound lateral resolution limit of about half of the wavelength of the detected light, i.e., within the range of 200 to 300 nm. The Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM) encompases a collection of image analysis techniques which rely on the statistical processing of temporal variations of fluorescence to reduce the uncertainty about the fluorophore positions within a sample, hence, bringing spatial resolution down to several tens of nm. The FF-SRM is known to be suitable for live-cell imaging due to its compatibility with most fluorescent probes and lower instrumental and experimental requirements, which are mostly camera-based epifluorescence instruments. Each FF-SRM approach has strengths and weaknesses, which depend directly on the underlying statistical principles through which enhanced spatial resolution is achieved. In this review, the basic concepts and principles behind a range of FF-SRM methods published to date are revisited. Their operational parameters are explained and guidance for its selection is provided.

bioinformatics↗

bioRxiv2020

Computer-assisted segmentation-free analysis for long-term assessment of flagellar beating in free swimming human spermatozoa: the role of emptying calcium stores

Microorganisms perform complex tasks and achieve biological function over long periods of time. Human spermatozoa are the archetype of long-time self-organizing transport in nature, and critical for reproductive success. They utilize the coordinated beating of their flagellum to swim long distances within the female reproductive tract in order to find and fertilize the egg. However, to this date, the long-time coordination of the sperm flagellum beating, or indeed other flagellated microorganisms, remain elusive due to limitations in microscope imaging and flagellar tracking techniques. Here, we present a novel methodology based on local orientation and isotropy of bio-image to obtain long-term kinematic and physiological parameters of individual free-swimming spermatozoa without requiring image segmentation (thresholding). This segmentation-free method allows for immediate evaluation of frequency and amplitude of the flagellar beat and head kinematic parameters for a duration of 9.2 min (limited by the cameras internal memory), corresponding to hundreds of thousands of flagellar beat cycles. We demonstrate the powerful use of this technique by examining how the release of Ca2+ from internal stores alters flagellar beating in the long-term, as Ca2+ is an essential regulator of flagellar beating. We report that increasing intracellular Ca2+ affected head and flagellar beat frequencies and amplitudes nonlinearly over long periods of time, commensurate with physiological conditions. The simplicity and robustness of the method may offer an advantageous alternative to segmentation-based methods, and allows for straightforward generalization to other bio-imaging applications, such as chlamydomonas, trypanosomes, c. elegans, or indeed flagellated microorganisms and slender-body organisms. Thus, this method may appeal to distant communities away from sperm biology.

cell biology↗

bioRxiv2019

The human sperm beats anisotropically and asymmetrically in 3D

The canonical beating of the human sperm flagellum is postulated to be symmetric. This is despite the reported asymmetries inherent to the flagellar axonemal structure, from distribution and activation of molecular motors to, even, the localisation of regulatory ion channels. This raises a fundamental question: how symmetric beating is possible within such intrinsically asymmetric flagellar complex? Here, we employ high-speed 3D imaging with mathematical analysis capable of resolving the flagellar movement in 4D (3D+time). This reveals that the human sperm beating is both anisotropic and asymmetric, and composed by a superposition of two transversal waves: an asymmetric travelling wave and a symmetric standing wave. This novel anisotropic travelling-pulsation mechanism induces sperm rolling self-organisation and causes a flagellar kinematic illusion, so that the beat appears to be symmetric if observed with 2D microscopy. The 3D beating anisotropy thus regularises the intrinsic flagellar asymmetry to achieve symmetric side-to-side movement and straight-line swimming.

cell biology↗