Beating against the clock

Zhang, Lilei; Jain, Mukesh K.

doi:10.1073/pnas.1601161113

Cited by 4 publications

(2 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently, our consortia published two high-quality reference genome sequences for the two main varietal groups of indica rice—Zhenshan 97 (ZS97) and Minghui 63 (MH63) ( Zhang et al , 2016a,b ). These genomes were primarily sequenced using PacBio long-read sequencing of minimum tiling path BAC pools, combined with Illumina WGS assembled contigs to fill gaps.…”

Section: Resultsmentioning

confidence: 99%

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences

Zhang

Kudrna

et al. 2016

Bioinformatics

View full text Add to dashboard Cite

Motivation: Next generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool—Genome Puzzle Master (GPM)—that enables the integration of additional genomic signposts to edit and build ‘new-gen-assemblies’ that result in high-quality ‘annotation-ready’ pseudomolecules. Results: With GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to ‘group,’ ‘merge,’ ‘order and orient’ sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user’s total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. Availability and Implementation: The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS Contacts: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.edu Supplementary information: Supplementary data are available at Bioinformatics online.

show abstract

Section: Resultsmentioning

confidence: 99%

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences

Zhang

Kudrna

et al. 2016

Bioinformatics

View full text Add to dashboard Cite

show abstract

“…S‐Nitrosoglutathione (GSNO) and S‐nitrosocysteine (CysNO) are often used to investigate the mechanism of cellular RSNO formation and transport. However, they require the assistance of a specific thiol or transporter . Recently, thionitrous acid (HSNO), the smallest RSNO, has received particular attention as a possible H 2 S‐derived signaling molecule .…”

Section: Methodsmentioning

confidence: 99%

Rational Design of a Dual‐Reactivity‐Based Fluorescent Probe for Visualizing Intracellular HSNO

et al. 2019

View full text Add to dashboard Cite

Thionitrous acid (HSNO), the smallest S‐nitrosothiol, is emerging as a potential key intermediate in cellular redox regulation linking two signaling molecules H2S and NO. However, the chemical biology of HSNO remains poorly understood. A major hurdle is the lack of methods for selective detection of HSNO in biological systems. Herein, we report the rational design, synthesis, and evaluation of the first fluorescent probe TAP‐1 for HSNO detection. TAP‐1 showed high selectivity and sensitivity to HSNO in aqueous media and cells, providing a useful tool for understanding the functions of HSNO in biology.

show abstract

Activity, sleep and ambient light have a different impact on circadian blood pressure, heart rate and body temperature rhythms

Gubin

Weinert

Rybina

et al. 2017

Chronobiology International

View full text Add to dashboard Cite

The aim of the present study was to investigate the impact of endogenous and exogenous factors for the expression of the daily rhythms of body temperature (BT), blood pressure (BP) and heart rate (HR). One hundred and seventy-three young adults (YA), 17-24 years old (y.o.), of both genders were studied under a modified constant-routine (CR) protocol for 26 h. Participants were assigned randomly to groups with different lighting regimens: CR-LD, n = 77, lights (>400 l×) on from 09:00 to 17:00 h and off (<10 l×) from 17:00 to 09:00 next morning; CR-LL, n = 81, lights on (>400 l×) during the whole experimental session; CR-DD, n = 15, constant dim light (<10 l×) during the whole experiment. Systolic (SBP) and diastolic (DBP) BP, HR and BT were measured every 2 h. For comparison, the results of the former studies performed under conditions of regular life with an activity period from 07:00 to 23:00 h and sleep from 23:00 till 07:00 h (Control) were reanalyzed. Seven-day Ambulatory Blood Pressure Monitoring (ABPM) records from 27 YA (16-38 y.o.) and BT self-measurement data from 70 YA (17-30 y.o.) taken on ≥ 3 successive days at 08:00, 11:00, 14:00, 17:00, 20:00, 23:00 and 03:00 were available. The obtained daily patterns were different between Control and CR-DD groups, due to effects of activity, sleep and light. The comparison of Control and CR-LD groups allowed the effects of sleep and activity to be estimated since the lighting conditions were similar. The activity level substantially elevated SBP, but not DBP. Sleep, on the other hand, lowered the nighttime DBP, but has no effect on SBP. HR was affected both by activity and sleep. In accordance with previous studies, these results confirm that the steep BP increase in the morning is not driven by the circadian clock, but rather by sympathoadrenal factors related to awakening and corresponding anticipatory mechanisms. The effect on BT was not significant. To investigate the impact of light during the former dark time and darkness during the former light time, the CR-LL and CR-DD groups were each compared with the CR-LD group. Light delayed the evening decrease of BT, most likely via a suppression of the melatonin rise. Besides, it had a prominent arousal effect on SBP both in the former light and dark phases, a moderate effect on DBP and no effect on HR. Darkness induced decline in BT. BP values were decreased during the former light time. No effects on HR were found. Altogether, the results of the present paper show that BT, BP and HR are affected by exogenous factors differently. Moreover, the effect was gender-specific. Especially, the response of BT and BP to ambient light was evident only in females. We suppose that the distinct, gender-specific responses of SBP, DBP and HR to activity, sleep and ambient light do reflect fundamental differences in the circadian control of various cardiovascular functions. Furthermore, the presented data are important for the elaboration of updated reference standards, the interpretation of rhythm disorders and for personalized...

show abstract

Beating against the clock

Cited by 4 publications

References 18 publications

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences

Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences

Rational Design of a Dual‐Reactivity‐Based Fluorescent Probe for Visualizing Intracellular HSNO

Activity, sleep and ambient light have a different impact on circadian blood pressure, heart rate and body temperature rhythms

Contact Info

Product

Resources

About